2 Datasets

2.1 Explanation of the data, origin and relevance.

Within the coursework for the subject “Knowledge Extraction from Biological Databases”, we extracted 4 datasets from the DepMap portal (https://depmap.org/portal/). The portal provides multiple datasets aiming to make various cancer cell line data openly available. It includes the Achilles project (gene essentiality across many cell lines) and the CCLE project (Cancer Cell Line Encyclopedia) which profiles genetic and pharmacological characteristics of many cancer models.

We were asked to use an RNA-seq expression dataset for protein-coding genes (raw_counts), which is our primary dataset. Specifically, the dataset corresponds to raw counts from the Achilles project and CCLE characterization data. We also used a Mutation Annotation Format (MAF)-based dataset representing mutations derived from VCF files produced at project level. This dataset (CCLE_mutations) is our secondary dataset. As metadata we used the drug_response dataset which measures viability of cell lines exposed to non-oncology compounds (log fold changes). Finally, sample_info contains information about the cell lines referenced in the other datasets.

2.2 Variable preparation

2.2.1 Dimensions and structure

raw_counts

## [1]  1379 52440
## 'data.frame':    1379 obs. of  52440 variables:
##  $ X                                          : chr  "ACH-001113" "ACH-001289" "ACH-001339" "ACH-001538" ...
##  $ TSPAN6..ENSG00000000003.                   : num  2383 2529 1552 5657 22806 ...
##  $ TNMD..ENSG00000000005.                     : num  0 13 0 0 0 5 0 0 0 0 ...
##  $ DPM1..ENSG00000000419.                     : num  4766 3857 8057 6056 4702 ...
##  $ SCYL3..ENSG00000000457.                    : num  962 555 849 1057 1109 ...
##  $ C1orf112..ENSG00000000460.                 : num  1518 833 2512 656 1500 ...
##  $ FGR..ENSG00000000938.                      : num  2 0 2 0 98 0 1 2 1 3 ...
##  $ CFH..ENSG00000000971.                      : num  162.8 19.1 201.8 7713 31296 ...
##  $ FUCA2..ENSG00000001036.                    : num  565 1000 13834 7928 5914 ...
##  $ GCLC..ENSG00000001084.                     : num  9078 1758 2189 3473 22393 ...
##  $ NFYA..ENSG00000001167.                     : num  4280 1684 2892 3378 4773 ...
##  $ STPG1..ENSG00000001460.                    : num  902 192 853 555 349 ...
##  $ NIPAL3..ENSG00000001461.                   : num  3364 1555 2923 4916 1127 ...
##  $ LAS1L..ENSG00000001497.                    : num  2276 2206 2436 4630 4639 ...
##  $ ENPP4..ENSG00000001561.                    : num  702 1841 210 2562 245 ...
##  $ SEMA3F..ENSG00000001617.                   : num  985 127 42 1173 10801 ...
##  $ CFTR..ENSG00000001626.                     : num  0 2 7 4 6 ...
##  $ ANKIB1..ENSG00000001629.                   : num  7618 7225 5936 4261 6102 ...
##  $ CYP51A1..ENSG00000001630.                  : num  10875 13374 8497 10992 19852 ...
##  $ KRIT1..ENSG00000001631.                    : num  4151 2423 3843 1604 3140 ...
##  $ RAD52..ENSG00000002016.                    : num  723 348 480 378 685 ...
##  $ MYH16..ENSG00000002079.                    : num  5 0 1 177 8 ...
##  $ BAD..ENSG00000002330.                      : num  812 996 792 1631 2862 ...
##  $ LAP3..ENSG00000002549.                     : num  1775 4528 7263 3411 5468 ...
##  $ CD99..ENSG00000002586.                     : num  1921 3205 16483 5631 8217 ...
##  $ HS3ST1..ENSG00000002587.                   : num  23 17 156 2364 2924 ...
##  $ AOC1..ENSG00000002726.                     : num  2 1 9 5 1 ...
##  $ WNT16..ENSG00000002745.                    : num  4 21 11 10 1 7 9 109 9 27 ...
##  $ HECW1..ENSG00000002746.                    : num  235 40 3 10 1 1 11 5 3 1 ...
##  $ MAD1L1..ENSG00000002822.                   : num  523 428 3075 1179 2498 ...
##  $ LASP1..ENSG00000002834.                    : num  6268 4195 18445 22524 32144 ...
##  $ SNX11..ENSG00000002919.                    : num  1489 1412 2563 1214 1823 ...
##  $ TMEM176A..ENSG00000002933.                 : num  0 1 6 2 0 ...
##  $ M6PR..ENSG00000003056.                     : num  14879 10859 21628 13951 18353 ...
##  $ KLHL13..ENSG00000003096.                   : num  4217 610 18 1 625 ...
##  $ CYP26B1..ENSG00000003137.                  : num  987 14 67 242 115 ...
##  $ ICA1..ENSG00000003147.                     : num  98 569 300 1078 3162 ...
##  $ DBNDD1..ENSG00000003249.                   : num  225 1041 1032 839 564 ...
##  $ ALS2..ENSG00000003393.                     : num  4261 2512 3562 1331 2762 ...
##  $ CASP10..ENSG00000003400.                   : num  362 21 214 1092 802 ...
##  $ CFLAR..ENSG00000003402.                    : num  3717 2329 3133 2825 4989 ...
##  $ TFPI..ENSG00000003436.                     : num  5 4 1524 615 85 ...
##  $ NDUFAF7..ENSG00000003509.                  : num  1518 844 1307 996 946 ...
##  $ RBM5..ENSG00000003756.                     : num  3522 6354 5124 5651 13458 ...
##  $ MTMR7..ENSG00000003987.                    : num  67.5 998.1 99.2 16.8 281.1 ...
##  $ SLC7A2..ENSG00000003989.                   : num  627 948 778 463 8211 ...
##  $ ARF5..ENSG00000004059.                     : num  3937 5066 4865 5098 8778 ...
##  $ SARM1..ENSG00000004139.                    : num  910 560 794 490 1645 ...
##  $ POLDIP2..ENSG00000004142.                  : num  4473 5112 8044 4381 8407 ...
##  $ PLXND1..ENSG00000004399.                   : num  3121 716 16777 118 727 ...
##  $ AK2..ENSG00000004455.                      : num  5782 5588 21212 17554 14712 ...
##  $ CD38..ENSG00000004468.                     : num  17 5 66 15 21 61 29 12 4 27 ...
##  $ FKBP4..ENSG00000004478.                    : num  13558 9604 8382 16632 15173 ...
##  $ KDM1A..ENSG00000004487.                    : num  4516 6694 6924 8978 7596 ...
##  $ RBM6..ENSG00000004534.                     : num  4403 4151 3612 4622 11895 ...
##  $ CAMKK1..ENSG00000004660.                   : num  1975 120 389 371 1307 ...
##  $ RECQL..ENSG00000004700.                    : num  6428 3426 11936 5962 4192 ...
##  $ VPS50..ENSG00000004766.                    : num  1960 1726 2663 1238 1398 ...
##  $ HSPB6..ENSG00000004776.                    : num  13 6.35 18.66 20.62 2 ...
##  $ ARHGAP33..ENSG00000004777.                 : num  456 587 161 91 631 ...
##  $ NDUFAB1..ENSG00000004779.                  : num  1726 2417 3305 5642 4286 ...
##  $ PDK4..ENSG00000004799.                     : num  0 0 347 837 224 ...
##  $ SLC22A16..ENSG00000004809.                 : num  1 4 3 1 0 0 0 1 1 1 ...
##  $ ZMYND10..ENSG00000004838.                  : num  23 79 24 6 15 35 9 120 268 23 ...
##  $ ABCB5..ENSG00000004846.                    : num  51 0 136 0 3 6 5 7 1 2 ...
##  $ ARX..ENSG00000004848.                      : num  1 33 8 0 6 3 877 1 1 8 ...
##  $ SLC25A13..ENSG00000004864.                 : num  758 2449 6220 2542 5473 ...
##  $ ST7..ENSG00000004866.                      : num  791 1904 2463 1532 1639 ...
##  $ CDC27..ENSG00000004897.                    : num  12186 6558 13839 8543 5757 ...
##  $ SLC4A1..ENSG00000004939.                   : num  7 0 0 2 1 0 0 0 0 10 ...
##  $ CALCR..ENSG00000004948.                    : num  6 27 2 3 5 2 10 0 0 11 ...
##  $ HCCS..ENSG00000004961.                     : num  1049 1480 2550 2870 2552 ...
##  $ DVL2..ENSG00000004975.                     : num  1615 3214 4376 1723 3177 ...
##  $ PRSS22..ENSG00000005001.                   : num  13 0 6 2506 1169 ...
##  $ UPF1..ENSG00000005007.                     : num  4928 3025 3969 4581 12645 ...
##  $ SKAP2..ENSG00000005020.                    : num  1406 91 11509 12761 4104 ...
##  $ SLC25A5..ENSG00000005022.                  : num  24646 15202 42244 43089 49243 ...
##  $ MCUB..ENSG00000005059.                     : num  190 5360 1038 1176 1533 ...
##  $ HOXA11..ENSG00000005073.                   : num  16.4 2 21 2 1013.4 ...
##  $ POLR2J..ENSG00000005075.                   : num  2455 2809 4882 1685 4629 ...
##  $ DHX33..ENSG00000005100.                    : num  6164 2193 5646 2293 4776 ...
##  $ MEOX1..ENSG00000005102.                    : num  1 0 0 0 0 4 1 0 2 1 ...
##  $ THSD7A..ENSG00000005108.                   : num  5 50 16 3 50 ...
##  $ LIG3..ENSG00000005156.                     : num  3678 6501 3007 1473 3835 ...
##  $ RPAP3..ENSG00000005175.                    : num  4348 2819 4411 2815 3401 ...
##  $ ACSM3..ENSG00000005187.                    : num  35.6 0.6 16.8 23.9 179.7 ...
##  $ REXO5..ENSG00000005189.                    : num  321 1564 862 1293 586 ...
##  $ CIAPIN1..ENSG00000005194.                  : num  3276 2750 5890 3176 4350 ...
##  $ SPPL2B..ENSG00000005206.                   : num  1333 539 903 783 3976 ...
##  $ FAM214B..ENSG00000005238.                  : num  1219 1211 1786 945 174 ...
##  $ COPZ2..ENSG00000005243.                    : num  58 0 2199 387 4 ...
##  $ PRKAR2B..ENSG00000005249.                  : num  578 2134 3902 102 110 ...
##  $ MSL3..ENSG00000005302.                     : num  1107 560 1492 2569 2880 ...
##  $ CREBBP..ENSG00000005339.                   : num  5318 3030 3435 3295 5221 ...
##  $ TSPOAP1..ENSG00000005379.                  : num  1 0 4 12 72 280 30 578 912 7 ...
##  $ MPO..ENSG00000005381.                      : num  0 0 0 0 3 29 4 57 88 9 ...
##  $ PON1..ENSG00000005421.                     : num  0 1 4 0 2 0 19 2 0 1 ...
##  $ GCFC2..ENSG00000005436.                    : num  961 1459 1897 1949 1713 ...
##  $ WDR54..ENSG00000005448.                    : num  445 614 1416 2798 1224 ...
##   [list output truncated]

The raw_counts dataset has 1379 rows (cell lines) and 52440 columns (genes). Cell lines are identified by “DepMapID” and genes by “Hugo Symbol” followed by “ENSEMBL id” in parentheses. All variables are numeric except “X1” which contains the cell line labels.

CCLE_mutations

## [1] 1288288      32
## 'data.frame':    1288288 obs. of  32 variables:
##  $ Hugo_Symbol           : chr  "VPS13D" "AADACL4" "IFNLR1" "TMEM57" ...
##  $ Entrez_Gene_Id        : int  55187 343066 163702 55219 7579 5453 23139 115361 10451 100288142 ...
##  $ NCBI_Build            : int  37 37 37 37 37 37 37 37 37 37 ...
##  $ Chromosome            : chr  "1" "1" "1" "1" ...
##  $ Start_position        : int  12359347 12726308 24484172 25785018 33954141 38512139 46498028 89657103 108247170 148346689 ...
##  $ End_position          : int  12359347 12726322 24484172 25785019 33954141 38512139 46498028 89657103 108247170 148346689 ...
##  $ Strand                : chr  "+" "+" "+" "+" ...
##  $ Variant_Classification: chr  "Nonsense_Mutation" "In_Frame_Del" "Silent" "Frame_Shift_Ins" ...
##  $ Variant_Type          : chr  "SNP" "DEL" "SNP" "INS" ...
##  $ Reference_Allele      : chr  "C" "CTGGCGTGACGCCAT" "G" "-" ...
##  $ Tumor_Seq_Allele1     : chr  "A" "-" "A" "A" ...
##  $ dbSNP_RS              : chr  "" "rs58218425|rs139261871|rs369427733|rs560787141" "" "" ...
##  $ dbSNP_Val_Status      : chr  "" "byFrequency" "" "" ...
##  $ Genome_Change         : chr  "g.chr1:12359347C>A" "g.chr1:12726308_12726322delCTGGCGTGACGCCAT" "g.chr1:24484172G>A" "g.chr1:25785018_25785019insA" ...
##  $ Annotation_Transcript : chr  "ENST00000358136.3" "ENST00000376221.1" "ENST00000327535.1" "ENST00000374343.4" ...
##  $ DepMap_ID             : chr  "ACH-000001" "ACH-000001" "ACH-000001" "ACH-000001" ...
##  $ cDNA_Change           : chr  "c.6122C>A" "c.786_800delCTGGCGTGACGCCAT" "c.1011C>T" "c.789_790insA" ...
##  $ Codon_Change          : chr  "c.(6121-6123)tCa>tAa" "c.(784-801)tcctggcgtgacgccatc>tcc" "c.(1009-1011)ggC>ggT" "c.(790-792)aaafs" ...
##  $ Protein_Change        : chr  "p.S2041*" "p.WRDAI263del" "p.G337G" "p.K264fs" ...
##  $ isDeleterious         : chr  "True" "False" "False" "True" ...
##  $ isTCGAhotspot         : chr  "False" "False" "False" "False" ...
##  $ TCGAhsCnt             : num  NA NA NA 0 NA 0 0 NA NA 0 ...
##  $ isCOSMIChotspot       : chr  "False" "False" "False" "False" ...
##  $ COSMIChsCnt           : num  0 3 0 0 0 0 0 0 0 0 ...
##  $ ExAC_AF               : num  NA NA NA NA NA ...
##  $ Variant_annotation    : chr  "damaging" "other non-conserving" "silent" "damaging" ...
##  $ CGA_WES_AC            : chr  "34:213" "57:141" "118:0" "" ...
##  $ HC_AC                 : chr  "" "" "" "" ...
##  $ RD_AC                 : chr  "" "" "" "" ...
##  $ RNAseq_AC             : chr  "" "" "" "6:28" ...
##  $ SangerWES_AC          : chr  "" "" "" "" ...
##  $ WGS_AC                : chr  "" "" "" "" ...

The CCLE_mutations dataset has 1,288,288 rows (mutations) and 32 descriptive columns. It contains identifiers (e.g., Entrez_Gene_Id, Hugo_Symbol, DepMap_ID) and mutation details (type, position, etc.). The first 11 columns represent part of the MAF format, while the remaining were added by CCLE (e.g., cDNA_Change, isDeleterious, Variant_annotation). DepMap_ID links the mutations to cell lines allowing joins with the other datasets.

drug_response

## [1]  578 4687
## 'data.frame':    578 obs. of  4687 variables:
##  $ X                                          : chr  "ACH-000001" "ACH-000007" "ACH-000008" "ACH-000010_FAILED_STR" ...
##  $ BRD.A00077618.236.07.6..2.5..HTS           : num  -0.0156 -0.0957 0.3795 0.1189 0.1453 ...
##  $ BRD.A00100033.001.08.9..2.5..HTS           : num  -0.449 0.258 -0.596 -0.232 -0.499 ...
##  $ BRD.A00147595.001.01.5..2.5..HTS           : num  0.489 0.772 0.548 0.622 0.267 ...
##  $ BRD.A00218260.001.03.4..2.5..HTS           : num  0.207 -0.439 0.422 -0.203 0.158 ...
##  $ BRD.A00376169.001.01.6..2.5..HTS           : num  0.273 -0.733 -0.217 -1.005 -0.272 ...
##  $ BRD.A00520476.001.07.4..2.5..HTS           : num  0.021 0.7792 0.0819 -0.2137 0.2078 ...
##  $ BRD.A00546892.001.02.6..2.5..HTS           : num  -0.02546 0.42652 0.14534 0.02025 0.00446 ...
##  $ BRD.A00578795.001.04.3..2.5..HTS           : num  0.467 -1.289 -0.571 -0.795 -0.192 ...
##  $ BRD.A00758722.001.04.9..2.5..HTS           : num  -0.736 -0.476 -0.512 NA -0.31 ...
##  $ BRD.A00827783.001.24.6..2.5..HTS           : num  0.644 -0.277 0.453 0.68 0.113 ...
##  $ BRD.A00993607.003.24.6..2.5..HTS           : num  -0.3711 -1.2491 0.2528 -0.0387 0.2683 ...
##  $ BRD.A01098288.001.02.9..2.5..HTS           : num  0.425 -0.525 0.174 -0.336 0.185 ...
##  $ BRD.A01412266.001.01.0..2.5..HTS           : num  NA 0.40064 0.00387 0.13676 -0.69812 ...
##  $ BRD.A01493904.003.12.1..2.5..HTS           : num  0.287 -0.7326 -0.0115 -0.7053 -0.0609 ...
##  $ BRD.A01563671.001.02.7..2.5..HTS           : num  0.4105 0.0659 0.4705 -0.0295 0.4257 ...
##  $ BRD.A01593789.001.03.1..2.5..HTS           : num  0.405 -1.1162 -0.0331 -0.1378 0.3738 ...
##  $ BRD.A01636364.003.15.1..2.5..HTS           : num  0.7023 0.527 0.0066 -0.1854 0.4973 ...
##  $ BRD.A01643550.001.04.9..2.5..HTS           : num  -0.6487 -1.6317 -0.0465 NA -0.3948 ...
##  $ BRD.A01787639.003.16.9..2.5..HTS           : num  0.53716 -0.57987 -0.27487 0.40747 -0.00193 ...
##  $ BRD.A01907367.001.01.7..2.5..HTS           : num  -0.0519 0.556 -0.4662 -0.1097 -0.3315 ...
##  $ BRD.A02006392.001.16.4..2.5..HTS           : num  -0.463 0.423 -0.446 -0.896 -0.39 ...
##  $ BRD.A02180903.001.04.5..2.5..HTS           : num  0.213 0.177 0.43 -0.397 0.408 ...
##  $ BRD.A02710418.003.11.8..2.5..HTS           : num  0.514 0.192 -0.354 -0.117 -0.441 ...
##  $ BRD.A02743701.001.03.6..2.5..HTS           : num  0.5616 -0.0157 0.1392 0.173 -0.1205 ...
##  $ BRD.A02759312.003.24.5..2.5..HTS           : num  0.0924 0.125 0.2828 -0.2759 0.4065 ...
##  $ BRD.A02990301.003.06.6..2.5..HTS           : num  -0.841 -0.365 -0.393 -0.659 -0.114 ...
##  $ BRD.A03061970.003.07.3..2.5..HTS           : num  0.61 0.24 0.149 -0.458 -0.124 ...
##  $ BRD.A03216249.003.24.3..2.5..HTS           : num  -1.401 -0.292 0.158 -0.544 -1.085 ...
##  $ BRD.A03359064.001.02.3..2.5..HTS           : num  0.774 -0.131 0.665 0.188 0.338 ...
##  $ BRD.A03506276.001.01.5..2.5..HTS           : num  -1.41 -2.57 -3.69 -3.3 -5.07 ...
##  $ BRD.A03623303.045.09.5..2.5..HTS           : num  -0.139 -0.366 -0.743 -0.597 -0.831 ...
##  $ BRD.A03880619.001.01.0..2.5..HTS           : num  0.266 -0.213 NA NA 0.195 ...
##  $ BRD.A03932035.004.04.3..2.5..HTS           : num  0.648 0.54 -0.147 NA -0.41 ...
##  $ BRD.A04203391.001.08.3..2.5..HTS           : num  -0.383 0.541 -0.297 -0.467 -0.268 ...
##  $ BRD.A04252265.003.01.4..2.5..HTS           : num  NA 0.5777 -0.0203 -0.5163 -0.0502 ...
##  $ BRD.A04322457.003.17.9..2.5..HTS           : num  0.0587 0.5525 -0.0493 0.6027 0.1814 ...
##  $ BRD.A04327189.001.15.1..2.5..HTS           : num  -0.329 0.066 -0.33 -0.235 -0.315 ...
##  $ BRD.A04327189.003.03.3..2.5..HTS           : num  0.228 0.543 0.194 NA 0.532 ...
##  $ BRD.A04352665.001.05.3..2.5..HTS           : num  0.213 0.283 0.528 NA 0.521 ...
##  $ BRD.A04497688.001.04.2..2.5..HTS           : num  0.179 0.48 0.123 0.611 0.354 ...
##  $ BRD.A04506385.001.01.2..2.5..HTS           : num  NA -0.3566 -0.2249 -0.1493 -0.0816 ...
##  $ BRD.A04553218.050.16.2..2.5..HTS           : num  0.3445 -0.0371 -0.0985 0.06 0.1954 ...
##  $ BRD.A04661934.001.02.9..2.5..HTS           : num  0.255 0.259 -0.176 0.135 0.109 ...
##  $ BRD.A05186015.003.19.8..2.5..HTS           : num  0.0909 0.5407 0.2209 0.1777 0.3522 ...
##  $ BRD.A05334458.001.02.8..2.5..HTS           : num  0.223 0.992 0.275 0.559 0.169 ...
##  $ BRD.A05457250.001.08.4..2.5..HTS           : num  -0.5334 -0.1141 -0.3143 -1.3938 0.0947 ...
##  $ BRD.A05515753.001.03.2..2.5..HTS           : num  0.0463 0.1645 0.0135 -0.2616 0.1079 ...
##  $ BRD.A05523972.001.01.5..2.5..HTS           : num  -0.0745 0.4815 0.3689 0.5272 -0.2871 ...
##  $ BRD.A05674712.001.06.0..2.5..HTS           : num  -0.2568 -0.7986 0.0222 NA 0.2414 ...
##  $ BRD.A05729358.001.02.0..2.5..HTS           : num  0.2683 0.4561 0.0127 0.2433 0.1397 ...
##  $ BRD.A05906449.004.01.1..2.5..HTS           : num  -0.209 -0.397 0.302 0.114 0.213 ...
##  $ BRD.A06352418.001.25.9..2.5..HTS           : num  -0.302 -1.052 -1.207 NA 0.193 ...
##  $ BRD.A06352508.001.03.7..2.5..HTS           : num  -0.191 -2.594 -0.925 -0.124 -0.161 ...
##  $ BRD.A06390036.001.04.6..2.5..HTS           : num  -0.1465 0.3022 -0.1323 -0.1116 0.0304 ...
##  $ BRD.A06426627.001.03.5..2.5..HTS           : num  0.616 -1.634 -0.289 -0.25 -0.642 ...
##  $ BRD.A06627858.236.03.0..2.5..HTS           : num  -1.54 -3.06 -3.52 -5.01 -2.15 ...
##  $ BRD.A06771424.004.01.7..2.5..HTS           : num  1.0642 0.5683 0.3165 -0.5771 0.0337 ...
##  $ BRD.A06916187.001.02.9..2.5..HTS           : num  -0.122 0.196 0.524 -0.195 0.176 ...
##  $ BRD.A06935312.001.04.3..2.5..HTS           : num  0.5016 0.905 0.2082 -0.1517 0.0261 ...
##  $ BRD.A07000685.001.04.4..2.5..HTS           : num  0.063 0.565 0.548 0.577 0.741 ...
##  $ BRD.A07164067.001.01.2..2.5..HTS           : num  -0.0156 -0.3998 -0.3246 0.1358 0.1764 ...
##  $ BRD.A07207424.001.13.2..2.5..HTS           : num  0.56 0.477 -0.512 -0.462 -0.522 ...
##  $ BRD.A07232941.001.02.7..2.5..HTS           : num  -0.2076 0.6881 0.0506 0.02 0.2224 ...
##  $ BRD.A07395371.003.10.0..2.5..HTS           : num  -0.2712 0.3746 0.0555 0.2218 0.559 ...
##  $ BRD.A07440155.003.25.4..2.5..HTS           : num  -0.218 0.474 0.204 0.568 0.397 ...
##  $ BRD.A07563059.035.01.3..2.5..HTS           : num  -0.188 0.979 0.268 0.333 0.337 ...
##  $ BRD.A07600638.060.05.2..2.5..HTS           : num  0.0809 -0.3191 0.1392 NA 0.1176 ...
##  $ BRD.A07704283.001.01.3..2.5..HTS           : num  0.577 0.716 0.142 -0.289 0.106 ...
##  $ BRD.A07780951.001.08.9..2.5..HTS           : num  -0.0392 -0.0235 0.3309 0.5397 0.0186 ...
##  $ BRD.A07780951.065.10.0..2.58..HTS          : num  0.872 -0.329 NA NA 0.479 ...
##  $ BRD.A07815743.001.01.1..2.5..HTS           : num  0.6981 -0.0198 0.2876 -0.6879 0.1377 ...
##  $ BRD.A07870296.001.07.4..2.5..HTS           : num  0.592 -0.0405 0.0565 0.5407 0.0993 ...
##  $ BRD.A07893380.213.01.7..2.5..HTS           : num  0.345 -0.407 0.24 NA 0.137 ...
##  $ BRD.A07932845.050.15.8..2.5..HTS           : num  0.0749 0.5231 -0.1526 -0.4104 0.2943 ...
##  $ BRD.A07947329.001.01.4..2.5..HTS           : num  0.3441 -0.3001 -0.2426 0.0326 -0.5534 ...
##  $ BRD.A07986123.001.02.8..2.5..HTS           : num  -0.302 -0.01 -0.189 NA -0.301 ...
##  $ BRD.A08079565.001.01.8..2.5..HTS           : num  -0.1685 -0.3897 -0.0983 -0.5774 -0.1868 ...
##  $ BRD.A08187463.001.12.9..2.5..HTS           : num  -0.684 -1.348 -0.343 NA -0.13 ...
##  $ BRD.A08255417.001.14.7..2.5..HTS           : num  -0.135 0.751 0.494 0.038 0.312 ...
##  $ BRD.A08302182.001.01.7..2.5..HTS           : num  0.3335 -0.6729 -0.0754 -0.6886 -0.1436 ...
##  $ BRD.A08545410.003.07.8..2.38..HTS          : num  0.0693 0.6077 1.1546 NA 0.6525 ...
##  $ BRD.A08545410.003.08.6..2.5..HTS           : num  1.095 -0.539 -0.167 -0.327 -0.086 ...
##  $ BRD.A08545410.311.01.8..2.5..HTS           : num  -0.0386 0.1407 -0.1815 NA 0.0935 ...
##  $ BRD.A08545410.311.03.4..2.5..HTS           : num  -1.209 -3.258 -0.924 NA -0.909 ...
##  $ BRD.A08660406.001.05.9..2.5..HTS           : num  0.0498 -1.3761 -0.7559 NA -0.0463 ...
##  $ BRD.A08715367.001.01.7..2.87..HTS          : num  0.151 0.328 -0.21 -1.394 -0.328 ...
##  $ BRD.A08840375.001.01.3..2.5..HTS           : num  -1.4 -3.34 -1.57 -2.5 -1.11 ...
##  $ BRD.A09056319.003.07.7..2.5..HTS           : num  -0.126 0.488 0.225 0.403 0.191 ...
##  $ BRD.A09062839.003.10.0..2.5..HTS           : num  -0.5967 0.5649 -0.4324 -0.4458 0.0947 ...
##  $ BRD.A09094913.065.01.0..2.5..HTS           : num  -0.4175 -0.2839 -0.0766 -0.6086 -0.4415 ...
##  $ BRD.A09349126.001.10.7..2.5..HTS           : num  1.407 -0.7497 0.0472 NA 0.1506 ...
##  $ BRD.A09370961.001.01.0..2.5..HTS           : num  0.66 -0.375 -1.089 NA -0.287 ...
##  $ BRD.A09467419.003.22.4..2.5..HTS           : num  0.1244 1.3703 0.1209 NA 0.0886 ...
##  $ BRD.A09472452.015.23.4..2.5..HTS           : num  -0.331 0.2393 -0.1565 NA 0.0392 ...
##  $ BRD.A09533288.003.31.2..2.5..HTS           : num  0.0396 -0.1382 -0.1224 NA 0.3315 ...
##  $ BRD.A09554849.236.07.6..2.5..HTS           : num  0.7528 0.5457 -0.0935 -0.4412 0.2627 ...
##  $ BRD.A09722536.002.18.0..2.5..HTS           : num  0.20442 -0.00205 0.13307 0.53681 0.46134 ...
##  $ BRD.A09735281.001.02.5..2.5..HTS           : num  -0.209 -0.616 0.109 -0.222 0.143 ...
##   [list output truncated]

The drug_response dataset has 578 rows (cell lines) and 4687 columns (drugs). It contains normalized log fold-change cell viability values per drug. Cell lines are identified by “DepMapID” and drugs by “Broad ID”. All variables are numeric except the “X” column which contains labels.

sample_info

## [1] 1811   26
## tibble [1,811 × 26] (S3: tbl_df/tbl/data.frame)
##  $ DepMap_ID                : chr [1:1811] "ACH-000001" "ACH-000002" "ACH-000003" "ACH-000004" ...
##  $ cell_line_name           : chr [1:1811] "NIH:OVCAR-3" "HL-60" "CACO2" "HEL" ...
##  $ stripped_cell_line_name  : chr [1:1811] "NIHOVCAR3" "HL60" "CACO2" "HEL" ...
##  $ CCLE_Name                : chr [1:1811] "NIHOVCAR3_OVARY" "HL60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE" "CACO2_LARGE_INTESTINE" "HEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE" ...
##  $ Alias                    : chr [1:1811] "OVCAR3" NA "CACO2, CaCo-2" NA ...
##  $ COSMICID                 : num [1:1811] 905933 905938 NA 907053 NA ...
##  $ sex                      : chr [1:1811] "Female" "Female" "Male" "Male" ...
##  $ source                   : chr [1:1811] "ATCC" "ATCC" "ATCC" "DSMZ" ...
##  $ Achilles_n_replicates    : num [1:1811] NA NA NA 2 2 NA 2 NA 3 NA ...
##  $ cell_line_NNMD           : num [1:1811] NA NA NA -3.08 -2.4 ...
##  $ culture_type             : chr [1:1811] NA NA NA "Suspension" ...
##  $ culture_medium           : chr [1:1811] NA NA NA "RPMI + 10% FBS" ...
##  $ cas9_activity            : num [1:1811] NA NA NA 52.4 86.6 NA 47.7 NA 94.2 NA ...
##  $ RRID                     : chr [1:1811] "CVCL_0465" "CVCL_0002" "CVCL_0025" "CVCL_0001" ...
##  $ WTSI_Master_Cell_ID      : num [1:1811] 2201 55 NA 783 NA ...
##  $ sample_collection_site   : chr [1:1811] "ascites" "haematopoietic_and_lymphoid_tissue" "Colon" "haematopoietic_and_lymphoid_tissue" ...
##  $ primary_or_metastasis    : chr [1:1811] "Metastasis" "Primary" NA NA ...
##  $ primary_disease          : chr [1:1811] "Ovarian Cancer" "Leukemia" "Colon/Colorectal Cancer" "Leukemia" ...
##  $ Subtype                  : chr [1:1811] "Adenocarcinoma, high grade serous" "Acute Myelogenous Leukemia (AML), M3 (Promyelocytic)" "Adenocarcinoma" "Acute Myelogenous Leukemia (AML), M6 (Erythroleukemia)" ...
##  $ age                      : num [1:1811] 60 35 NA 30 30 64 63 56 72 NA ...
##  $ Sanger_Model_ID          : chr [1:1811] "SIDM00105" "SIDM00829" "SIDM00891" "SIDM00594" ...
##  $ depmap_public_comments   : logi [1:1811] NA NA NA NA NA NA ...
##  $ lineage                  : chr [1:1811] "ovary" "blood" "colorectal" "blood" ...
##  $ lineage_subtype          : chr [1:1811] "ovary_adenocarcinoma" "AML" "colorectal_adenocarcinoma" "AML" ...
##  $ lineage_sub_subtype      : chr [1:1811] "high_grade_serous" "M3" NA "M6" ...
##  $ lineage_molecular_subtype: chr [1:1811] NA NA NA NA ...

The sample_info dataset has 1811 rows (cell lines) and 26 descriptive columns, including identifiers (DepMap_ID, COSMICID, CCLE_Name), cell line features (source, culture_type, lineage), and donor info (sex, age). DepMap_ID is key to relate datasets.

2.2.2 Curation

# process sample_info
# Set as characters
sample_info$COSMICID <- as.character(sample_info$COSMICID)
sample_info$WTSI_Master_Cell_ID <- as.character(sample_info$WTSI_Master_Cell_ID)

# Set as factors
sample_info$sex <- as.factor(sample_info$sex)
sample_info$source <- as.factor(sample_info$source)
sample_info$culture_type <- as.factor(sample_info$culture_type)
sample_info$sample_collection_site <- as.factor(sample_info$sample_collection_site)
sample_info$primary_or_metastasis <- as.factor(sample_info$primary_or_metastasis)
sample_info$primary_disease <- as.factor(sample_info$primary_disease)
sample_info$Subtype <- as.factor(sample_info$Subtype)
sample_info$lineage <- as.factor(sample_info$lineage)
sample_info$lineage_subtype <- as.factor(sample_info$lineage_subtype)
sample_info$lineage_sub_subtype <- as.factor(sample_info$lineage_sub_subtype)
sample_info$lineage_molecular_subtype <- as.factor(sample_info$lineage_molecular_subtype)

# process mutations dataset
# Set as characters
CCLE_mutations$Hugo_Symbol <- as.character(CCLE_mutations$Hugo_Symbol)
CCLE_mutations$Entrez_Gene_Id <- as.character(CCLE_mutations$Entrez_Gene_Id)
CCLE_mutations$NCBI_Build <- as.character(CCLE_mutations$NCBI_Build)

# Set as factors
CCLE_mutations$Strand <- as.factor(CCLE_mutations$Strand)
CCLE_mutations$Variant_Classification <- as.factor(CCLE_mutations$Variant_Classification)
CCLE_mutations$Variant_Type <- as.factor(CCLE_mutations$Variant_Type)
CCLE_mutations$dbSNP_Val_Status <- as.factor(CCLE_mutations$dbSNP_Val_Status)
CCLE_mutations$DepMap_ID <- as.factor(CCLE_mutations$DepMap_ID)
CCLE_mutations$Variant_annotation <- as.factor(CCLE_mutations$Variant_annotation)

After identifying variable types we performed manual curation to ensure correct formats for statistical analysis. Several character columns were factorized (e.g., sex), and some numeric-looking identifiers were converted to character (e.g., Hugo_Symbol). Missing values in some non-numeric variables were left as-is or handled later if needed.

3 Pre-processing

3.1 Missing values handling

## [1] 0
## [1] 1955870
## [1] 76337
## [1] 14818

We found NAs in sample_info, drug_response and CCLE_mutation. Only drug_response’s NAs (numeric) need immediate treatment because many downstream methods cannot handle NAs. For drug_response we imputed column-wise mean values for NA entries, reasoning that replacing missing responses for a drug with that drug’s mean is more appropriate than using a gene-wise mean.

## [1] 0

4 Data summarization

4.1 Variable summary

CCLE_mutations

No Variable Stats / Values Freqs (% of Valid) Graph Missing
1 Hugo_Symbol [character]
1. TTN
2. MUC16
3. TP53
4. OBSCN
5. RYR2
[ 19334 others ]
1915(0.4%)
999(0.2%)
478(0.1%)
460(0.1%)
440(0.1%)
495027(99.1%)
0 (0.0%)
2 Entrez_Gene_Id [character]
1. 0
2. 7273
3. 94025
4. 7157
5. 84033
[ 18675 others ]
6708(1.3%)
1915(0.4%)
999(0.2%)
478(0.1%)
460(0.1%)
488759(97.9%)
0 (0.0%)
3 NCBI_Build [character] 1. 37
499319(100.0%)
0 (0.0%)
4 Chromosome [character]
1. 1
2. 2
3. 19
4. 11
5. 3
[ 20 others ]
50854(10.2%)
37427(7.5%)
35688(7.1%)
30625(6.1%)
27820(5.6%)
316905(63.5%)
0 (0.0%)
5 Start_position [integer]
Mean (sd) : 77328857 (58101096)
min ≤ med ≤ max:
3308 ≤ 61895677 ≤ 249212542
IQR (CV) : 84394070 (0.8)
460934 distinct values 0 (0.0%)
6 End_position [integer]
Mean (sd) : 77328857 (58101096)
min ≤ med ≤ max:
3308 ≤ 61895677 ≤ 249212542
IQR (CV) : 84394070 (0.8)
459239 distinct values 0 (0.0%)
7 Strand [factor] 1. +
499319(100.0%)
0 (0.0%)
8 Variant_Classification [factor]
1. 3'UTR
2. 5'Flank
3. 5'UTR
4. De_novo_Start_OutOfFrame
5. Frame_Shift_Del
[ 15 others ]
48(0.0%)
60(0.0%)
27(0.0%)
2629(0.5%)
22075(4.4%)
474480(95.0%)
0 (0.0%)
9 Variant_Type [factor]
1. DEL
2. DNP
3. INS
4. SNP
5. TNP
26962(5.4%)
377(0.1%)
15748(3.2%)
456230(91.4%)
2(0.0%)
0 (0.0%)
10 Reference_Allele [character]
1. C
2. G
3. T
4. A
5. -
[ 1992 others ]
173900(34.8%)
172694(34.6%)
65049(13.0%)
64645(12.9%)
15748(3.2%)
7283(1.5%)
0 (0.0%)
11 Tumor_Seq_Allele1 [character]
1. A
2. T
3. C
4. G
5. -
[ 567 others ]
167407(33.5%)
167342(33.5%)
68155(13.6%)
66943(13.4%)
26962(5.4%)
2510(0.5%)
0 (0.0%)
12 dbSNP_RS [character]
1. (Empty string)
2. rs121913529
3. rs149639659
4. rs121913377|rs113488022|r
5. rs140898828
[ 63758 others ]
424086(84.9%)
70(0.0%)
54(0.0%)
51(0.0%)
37(0.0%)
75021(15.0%)
0 (0.0%)
13 dbSNP_Val_Status [factor]
1. (Empty string)
2. byFrequency
484823(97.1%)
14496(2.9%)
0 (0.0%)
14 Genome_Change [character]
1. g.chr21:32127496_32127497
2. g.chr7:140453136A>T
3. g.chr12:25398284C>T
4. g.chr1:6257785delT
5. g.chr19:54675769_54675771
[ 464410 others ]
54(0.0%)
50(0.0%)
37(0.0%)
36(0.0%)
36(0.0%)
499106(100.0%)
0 (0.0%)
15 Annotation_Transcript [character]
1. ENST00000589042.1
2. ENST00000397910.4
3. ENST00000269305.4
4. ENST00000366574.2
5. ENST00000367255.5
[ 23991 others ]
1703(0.3%)
999(0.2%)
450(0.1%)
440(0.1%)
415(0.1%)
495312(99.2%)
0 (0.0%)
16 DepMap_ID [factor]
1. ACH-000001
2. ACH-000002
3. ACH-000003
4. ACH-000004
5. ACH-000005
[ 1742 others ]
308(0.1%)
0(0.0%)
0(0.0%)
0(0.0%)
0(0.0%)
499011(99.9%)
0 (0.0%)
17 cDNA_Change [character]
1. (Empty string)
2. c.2T>C
3. c.1A>G
4. c.3G>A
5. c.4G>A
[ 89222 others ]
12521(2.5%)
142(0.0%)
140(0.0%)
136(0.0%)
121(0.0%)
486259(97.4%)
0 (0.0%)
18 Codon_Change [character]
1. (Empty string)
2. c.e2-1
3. c.e1+1
4. c.e4-1
5. c.e3-1
[ 271592 others ]
3359(0.7%)
437(0.1%)
385(0.1%)
359(0.1%)
346(0.1%)
494433(99.0%)
0 (0.0%)
19 Protein_Change [character]
1. (Empty string)
2. p.M1I
3. p.M1T
4. p.M1V
5. p.A2A
[ 175473 others ]
12524(2.5%)
215(0.0%)
139(0.0%)
137(0.0%)
71(0.0%)
486233(97.4%)
0 (0.0%)
20 isDeleterious [character]
1. (Empty string)
2. False
3. True
1(0.0%)
423638(84.8%)
75680(15.2%)
0 (0.0%)
21 isTCGAhotspot [character]
1. False
2. True
485219(97.2%)
14100(2.8%)
0 (0.0%)
22 TCGAhsCnt [numeric]
Mean (sd) : 1.5 (23.3)
min ≤ med ≤ max:
0 ≤ 0 ≤ 784
IQR (CV) : 0 (16)
78 distinct values 360019 (72.1%)
23 isCOSMIChotspot [character]
1. (Empty string)
2. False
3. True
1(0.0%)
497653(99.7%)
1665(0.3%)
0 (0.0%)
24 COSMIChsCnt [numeric]
Mean (sd) : 4.9 (253.8)
min ≤ med ≤ max:
0 ≤ 0 ≤ 24231
IQR (CV) : 0 (51.4)
233 distinct values 25 (0.0%)
25 ExAC_AF [numeric]
Mean (sd) : 0 (0)
min ≤ med ≤ max:
0 ≤ 0 ≤ 0
IQR (CV) : 0 (4)
3781 distinct values 390013 (78.1%)
26 Variant_annotation [factor]
1. damaging
2. other conserving
3. other non-conserving
4. silent
75234(15.1%)
490(0.1%)
294925(59.1%)
128670(25.8%)
0 (0.0%)
27 CGA_WES_AC [character]
1. (Empty string)
2. 5:7
3. 6:8
4. 7:9
5. 4:5
[ 44785 others ]
128872(25.8%)
268(0.1%)
251(0.1%)
251(0.1%)
248(0.0%)
369429(74.0%)
0 (0.0%)
28 HC_AC [character]
1. (Empty string)
2. 3:3
3. 3:1
4. 3:2
5. 3:4
[ 5482 others ]
490648(98.3%)
32(0.0%)
31(0.0%)
28(0.0%)
24(0.0%)
8556(1.7%)
0 (0.0%)
29 RD_AC [character]
1. (Empty string)
2. 100:170
3. 1000:492
4. 101:332
5. 101:49
[ 229 others ]
499086(100.0%)
1(0.0%)
1(0.0%)
1(0.0%)
1(0.0%)
229(0.0%)
0 (0.0%)
30 RNAseq_AC [character]
1. (Empty string)
2. 4:4
3. 4:5
4. 4:7
5. 4:6
[ 14364 others ]
465168(93.2%)
155(0.0%)
138(0.0%)
116(0.0%)
113(0.0%)
33629(6.7%)
0 (0.0%)
31 SangerWES_AC [character]
1. (Empty string)
2. 4:0
3. 6:4
4. 5:0
5. 6:2
[ 9159 others ]
477109(95.6%)
62(0.0%)
55(0.0%)
52(0.0%)
49(0.0%)
21992(4.4%)
0 (0.0%)
32 WGS_AC [character]
1. (Empty string)
2. 14:15
3. 16:17
4. 14:17
5. 16:16
[ 3584 others ]
435712(87.3%)
204(0.0%)
199(0.0%)
198(0.0%)
195(0.0%)
62811(12.6%)
0 (0.0%)

Generated by summarytools 1.1.4 (R version 4.5.1)
2025-08-28

After cleaning variable types we computed descriptive statistics for sub_sample_info and sub_CCLE_mutations. We omitted summaries for sub_raw_counts and sub_drug_response due to the high number of numeric variables and computational cost. For sub_CCLE_mutations: chromosome 1 is the most frequent (~10%); Variant_Classification shows Missense_Mutation (~58%) and Silent (~25%); Variant_Type is mostly SNP (~91%). Some annotation columns have many missing values (dbSNP), and some added CCLE columns have many unique values and many missing entries.

Back to summary

sample_info

No Variable Stats / Values Freqs (% of Valid) Graph Missing
1 DepMap_ID [character]
1. ACH-000001
2. ACH-000007
3. ACH-000008
4. ACH-000011
5. ACH-000012
[ 554 others ]
1(0.2%)
1(0.2%)
1(0.2%)
1(0.2%)
1(0.2%)
554(99.1%)
0 (0.0%)
2 cell_line_name [character]
1. 22Rv1
2. 23132/87
3. 253J
4. 253J-BV
5. 42-MG-BA
[ 554 others ]
1(0.2%)
1(0.2%)
1(0.2%)
1(0.2%)
1(0.2%)
554(99.1%)
0 (0.0%)
3 stripped_cell_line_name [character]
1. 22RV1
2. 2313287
3. 253J
4. 253JBV
5. 42MGBA
[ 554 others ]
1(0.2%)
1(0.2%)
1(0.2%)
1(0.2%)
1(0.2%)
554(99.1%)
0 (0.0%)
4 CCLE_Name [character]
1. 22RV1_PROSTATE
2. 2313287_STOMACH
3. 253J_URINARY_TRACT
4. 253JBV_URINARY_TRACT
5. 42MGBA_CENTRAL_NERVOUS_SY
[ 554 others ]
1(0.2%)
1(0.2%)
1(0.2%)
1(0.2%)
1(0.2%)
554(99.1%)
0 (0.0%)
5 Alias [character]
1. 22-RV1
2. A101D, Hs 294.T
3. CADO-ES-1
4. CB-AGPN
5. COR-L23/CPR
[ 12 others ]
1(5.9%)
1(5.9%)
1(5.9%)
1(5.9%)
1(5.9%)
12(70.6%)
542 (97.0%)
6 COSMICID [character]
1. 1240121
2. 1240123
3. 1240125
4. 1240127
5. 1240128
[ 390 others ]
1(0.3%)
1(0.3%)
1(0.3%)
1(0.3%)
1(0.3%)
390(98.7%)
164 (29.3%)
7 sex [factor]
1. Female
2. Male
3. Unknown
231(41.3%)
298(53.3%)
30(5.4%)
0 (0.0%)
8 source [factor]
1. Academic lab
2. Asterand
3. ATCC
4. Cancer Cell Line Factory
5. CellBank Australia
[ 18 others ]
23(4.1%)
0(0.0%)
230(41.1%)
2(0.4%)
0(0.0%)
304(54.4%)
0 (0.0%)
9 Achilles_n_replicates [numeric]
Mean (sd) : 2.1 (0.8)
min ≤ med ≤ max:
0 ≤ 2 ≤ 4
IQR (CV) : 0 (0.4)
0:23(5.2%)
1:32(7.3%)
2:297(67.7%)
3:64(14.6%)
4:23(5.2%)
120 (21.5%)
10 cell_line_NNMD [numeric]
Mean (sd) : -3.7 (1.1)
min ≤ med ≤ max:
-6.5 ≤ -3.7 ≤ -0.2
IQR (CV) : 1.6 (-0.3)
439 distinct values 120 (21.5%)
11 culture_type [factor]
1. Adherent
2. Adherent and floating via
3. Loosely Adherent
4. Mix (loosely adherent wit
5. Mixed
[ 4 others ]
282(90.4%)
0(0.0%)
0(0.0%)
0(0.0%)
0(0.0%)
30(9.6%)
247 (44.2%)
12 culture_medium [character]
1. RPMI + 10% FBS
2. DMEM + 10% FBS
3. EMEM + 10% FBS
4. McCoy's 5A + 10% FBS
5. not found
[ 83 others ]
174(39.7%)
54(12.3%)
31(7.1%)
15(3.4%)
14(3.2%)
150(34.2%)
121 (21.6%)
13 cas9_activity [numeric]
Mean (sd) : 74.9 (15.3)
min ≤ med ≤ max:
30.3 ≤ 79.8 ≤ 97.8
IQR (CV) : 23.6 (0.2)
292 distinct values 123 (22.0%)
14 RRID [character]
1. CVCL_0021
2. CVCL_0022
3. CVCL_0023
4. CVCL_0026
5. CVCL_0027
[ 552 others ]
1(0.2%)
1(0.2%)
1(0.2%)
1(0.2%)
1(0.2%)
552(99.1%)
2 (0.4%)
15 WTSI_Master_Cell_ID [character]
1. 1
2. 1001
3. 1005
4. 1007
5. 1011
[ 390 others ]
1(0.3%)
1(0.3%)
1(0.3%)
1(0.3%)
1(0.3%)
390(98.7%)
164 (29.3%)
16 sample_collection_site [factor]
1. abdomen
2. ascites
3. autonomic_ganglia
4. biliary_tract
5. bone
[ 36 others ]
1(0.2%)
32(5.7%)
4(0.7%)
6(1.1%)
14(2.5%)
502(89.8%)
0 (0.0%)
17 primary_or_metastasis [factor]
1. Metastasis
2. Primary
202(41.0%)
291(59.0%)
66 (11.8%)
18 primary_disease [factor]
1. Adrenal Cancer
2. Bile Duct Cancer
3. Bladder Cancer
4. Bone Cancer
5. Brain Cancer
[ 30 others ]
0(0.0%)
6(1.1%)
24(4.3%)
18(3.2%)
42(7.5%)
469(83.9%)
0 (0.0%)
19 Subtype [factor]
1. Acute Biphenotypic Leukem
2. Acute Lymphoblastic Leuke
3. Acute Lymphoblastic Leuke
4. Acute Myelogenous Leukemi
5. Acute Myelogenous Leukemi
[ 168 others ]
0(0.0%)
0(0.0%)
0(0.0%)
0(0.0%)
0(0.0%)
544(100.0%)
15 (2.7%)
20 age [numeric]
Mean (sd) : 53 (18.1)
min ≤ med ≤ max:
0.2 ≤ 56 ≤ 88
IQR (CV) : 20 (0.3)
77 distinct values 142 (25.4%)
21 Sanger_Model_ID [character]
1. SIDM00008
2. SIDM00011
3. SIDM00015
4. SIDM00027
5. SIDM00032
[ 442 others ]
1(0.2%)
1(0.2%)
1(0.2%)
1(0.2%)
1(0.2%)
442(98.9%)
112 (20.0%)
22 depmap_public_comments [logical]
All NA's
559 (100.0%)
23 lineage [factor]
1. adrenal_cortex
2. bile_duct
3. blood
4. bone
5. breast
[ 34 others ]
0(0.0%)
7(1.3%)
0(0.0%)
18(3.2%)
26(4.7%)
508(90.9%)
0 (0.0%)
24 lineage_subtype [factor]
1. acute_biphenotypic_leukem
2. adrenal_carcinoma
3. ALL
4. AML
5. ATL
[ 99 others ]
0(0.0%)
0(0.0%)
0(0.0%)
0(0.0%)
0(0.0%)
558(100.0%)
1 (0.2%)
25 lineage_sub_subtype [factor]
1. acral
2. alveolar
3. amelanotic
4. anaplastic
5. astrocytoma
[ 76 others ]
0(0.0%)
1(0.3%)
2(0.7%)
2(0.7%)
10(3.5%)
272(94.8%)
272 (48.7%)
26 lineage_molecular_subtype [factor]
1. basal
2. basal_A
3. basal_B
4. EWS_ERG
5. EWS_FEV
[ 10 others ]
0(0.0%)
8(13.6%)
7(11.9%)
1(1.7%)
0(0.0%)
43(72.9%)
500 (89.4%)

Generated by summarytools 1.1.4 (R version 4.5.1)
2025-08-28

For sub_sample_info: sex distribution ~41% Female, 53% Male, 5% Unknown. Source labs show top providers (ATCC, DSMZ, HSRRB). Mean number of replicates ~2.1. Culture type mainly Adherent (~90%). cas9_activity mean ~74.9 (SD 15.3). primary_or_metastasis distribution Primary 59%, Metastasis 41%. Age mean 53. Many missing entries in some variables.

Back to summary

4.2 Plots supporting summary

## Levene's Test for Homogeneity of Variance (center = median)
##        Df F value Pr(>F)
## group   2  0.8271  0.438
##       414
##                      Df Sum Sq Mean Sq F value Pr(>F)
## sub_sample_info$sex   2    542   270.8   0.826  0.438
## Residuals           414 135683   327.7               
## 142 observations deleted due to missingness

We created pie charts for Variant_Type and Variant_annotation, performed ANOVA on age vs sex (no significant difference), and plotted boxplot and histogram for supporting visuals.

5 Differential expression

5.1 Metadata preparation

To run differential expression we selected metadata: primary_or_metastasis (type) and a derived variable mut_counts (count of mutations per cell line) from CCLE_mutations.

## Descriptive Statistics  
## mutation_counts$mut_freq  
## N: 1747  
## 
##                     mut_freq
## ----------------- ----------
##              Mean     737.43
##           Std.Dev    2163.49
##               Min      16.00
##                Q1     249.00
##            Median     367.00
##                Q3     577.00
##               Max   66665.00
##               MAD     207.56
##               IQR     326.50
##                CV       2.93
##          Skewness      19.42
##       SE.Skewness       0.06
##          Kurtosis     525.69
##           N.Valid    1747.00
##                 N    1747.00
##         Pct.Valid     100.00
## 'data.frame':    1747 obs. of  2 variables:
##  $ mut_freq  : int  308 180 207 271 288 220 408 379 438 352 ...
##  $ mut_counts: Factor w/ 3 levels "Low","Medium",..: 2 1 1 1 1 1 2 2 2 2 ...
##   ..- attr(*, "discretized:breaks")= num [1:4] 16 290 477 66665
##   ..- attr(*, "discretized:method")= chr "frequency"
## Frequencies  
## mutation_counts$mut_counts  
## Type: Factor  
## 
##                Freq   % Valid   % Valid Cum.   % Total   % Total Cum.
## ------------ ------ --------- -------------- --------- --------------
##          Low    582     33.31          33.31     33.31          33.31
##       Medium    581     33.26          66.57     33.26          66.57
##         High    584     33.43         100.00     33.43         100.00
##         <NA>      0                               0.00         100.00
##        Total   1747    100.00         100.00    100.00         100.00
## Error in match(x, table, nomatch = 0L): 'match' requires vector arguments
## Warning in parse_call(mc = match.call(), caller = "freq"): metadata extraction
## terminated unexpectedly; inspect results carefully
## Frequencies  
## 
##                    Freq   % Valid   % Valid Cum.   % Total   % Total Cum.
## ---------------- ------ --------- -------------- --------- --------------
##       Metastasis    498     43.42          43.42     27.50          27.50
##          Primary    649     56.58         100.00     35.84          63.34
##             <NA>    664                              36.66         100.00
##            Total   1811    100.00         100.00    100.00         100.00
## Data Frame Summary  
## clean_metadados  
## Dimensions: 1125 x 4  
## Duplicates: 0  
## 
## --------------------------------------------------------------------------------------------------------------
## No   Variable      Stats / Values             Freqs (% of Valid)    Graph                 Valid      Missing  
## ---- ------------- -------------------------- --------------------- --------------------- ---------- ---------
## 1    Row.names     1. ACH-000001                 1 ( 0.1%)                                1125       0        
##      [character]   2. ACH-000002                 1 ( 0.1%)                                (100.0%)   (0.0%)   
##                    3. ACH-000006                 1 ( 0.1%)                                                    
##                    4. ACH-000007                 1 ( 0.1%)                                                    
##                    5. ACH-000009                 1 ( 0.1%)                                                    
##                    6. ACH-000011                 1 ( 0.1%)                                                    
##                    7. ACH-000012                 1 ( 0.1%)                                                    
##                    8. ACH-000013                 1 ( 0.1%)                                                    
##                    9. ACH-000014                 1 ( 0.1%)                                                    
##                    10. ACH-000015                1 ( 0.1%)                                                    
##                    [ 1115 others ]            1115 (99.1%)          IIIIIIIIIIIIIIIIIII                       
## 
## 2    mut_freq      Mean (sd) : 812.5 (2313)   672 distinct values   :                     1125       0        
##      [integer]     min < med < max:                                 :                     (100.0%)   (0.0%)   
##                    16 < 421 < 66665                                 :                                         
##                    IQR (CV) : 356 (2.8)                             :                                         
##                                                                     :                                         
## 
## 3    mut_counts    1. Low                     270 (24.0%)           IIII                  1125       0        
##      [factor]      2. Medium                  389 (34.6%)           IIIIII                (100.0%)   (0.0%)   
##                    3. High                    466 (41.4%)           IIIIIIII                                  
## 
## 4    type          1. Metastasis              483 (42.9%)           IIIIIIII              1125       0        
##      [factor]      2. Primary                 642 (57.1%)           IIIIIIIIIII           (100.0%)   (0.0%)   
## --------------------------------------------------------------------------------------------------------------
## [1]  1020 52440
## [1] 1020    4

We counted mutations per DepMap_ID to produce mut_freq and discretized into mut_counts with three roughly equally-sized bins: Low, Medium, High. type is taken from primary_or_metastasis and entries with NA were omitted. The resulting clean_metadados and meta_expression were intersected to produce matched expression and metadata for differential analysis.

5.2 Univariate analysis on metadata

We explored the metadata with descriptive stats and non-parametric tests where appropriate.

## Descriptive Statistics  
## mutation_counts$mut_freq  
## N: 1747  
## 
##                     mut_freq
## ----------------- ----------
##              Mean     737.43
##           Std.Dev    2163.49
##               Min      16.00
##                Q1     249.00
##            Median     367.00
##                Q3     577.00
##               Max   66665.00
##               MAD     207.56
##               IQR     326.50
##                CV       2.93
##          Skewness      19.42
##       SE.Skewness       0.06
##          Kurtosis     525.69
##           N.Valid    1747.00
##                 N    1747.00
##         Pct.Valid     100.00

## 
##  Shapiro-Wilk normality test
## 
## data:  clean_metadados$mut_freq
## W = 0.18291, p-value < 2.2e-16
## Levene's Test for Homogeneity of Variance (center = median)
##         Df F value Pr(>F)
## group    1  0.1588 0.6903
##       1123
## Levene's Test for Homogeneity of Variance (center = median)
##         Df F value   Pr(>F)    
## group    2  22.523 2.57e-10 ***
##       1122                     
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
##  Wilcoxon rank sum test with continuity correction
## 
## data:  clean_metadados$mut_freq by clean_metadados$type
## W = 160234, p-value = 0.3359
## alternative hypothesis: true location shift is not equal to 0

## 
##  Kruskal-Wallis rank sum test
## 
## data:  clean_metadados$mut_freq by clean_metadados$mut_counts
## Kruskal-Wallis chi-squared = 982.11, df = 2, p-value < 2.2e-16
## 
##  Pairwise comparisons using Wilcoxon rank sum test with continuity correction 
## 
## data:  clean_metadados$mut_freq and clean_metadados$mut_counts 
## 
##        Low    Medium
## Medium <2e-16 -     
## High   <2e-16 <2e-16
## 
## P value adjustment method: BH

mut_freq is not normally distributed (Shapiro), so non-parametric tests were used: Wilcox for two-group comparisons and Kruskal-Wallis for three-group comparisons (followed by pairwise Wilcox with BH correction). Significant differences were observed across mut_counts groups.

5.5 Differential expression analysis

We used the limma pipeline for differential expression analysis. First, we filtered out lowly expressed genes.

5.5.1 Metadata preparation

We used the same metadata as in the previous analysis.

5.5.3 GO enrichment analysis

We performed GO enrichment analysis on the differentially expressed genes.

##     query significant     p_value term_size query_size intersection_size
## 1 query_1        TRUE 0.001449914        74          7                 3
## 2 query_1        TRUE 0.001510111        75          7                 3
## 3 query_1        TRUE 0.039392389       222          7                 3
##   precision     recall    term_id source
## 1 0.4285714 0.04054054 GO:0071260  GO:BP
## 2 0.4285714 0.04000000 GO:0071496  GO:BP
## 3 0.4285714 0.01351351 GO:0009612  GO:BP
##                                  term_name effective_domain_size source_order
## 1 cellular response to mechanical stimulus                 21026        16288
## 2   cellular response to external stimulus                 21026        16498
## 3          response to mechanical stimulus                 21026         3526
##        parents
## 1 GO:00096....
## 2   GO:0009605
## 3 GO:00096....

GO analysis showed mainly underexpression of immune response and stimulus response terms for metastasis vs primary.

Back to analysis

Mutation_count

##            Low Medium High
## ACH-000001   0      1    0
## ACH-000002   1      0    0
## ACH-000006   1      0    0
## ACH-000007   0      1    0
## ACH-000009   0      1    0
## ACH-000011   0      1    0
## ACH-000012   1      0    0
## ACH-000013   1      0    0
## ACH-000014   0      0    1
## ACH-000015   0      1    0
## ACH-000016   1      0    0
## ACH-000017   0      1    0
## ACH-000018   1      0    0
## ACH-000019   0      0    1
## ACH-000021   0      1    0
## ACH-000022   1      0    0
## ACH-000023   0      1    0
## ACH-000024   0      0    1
## ACH-000026   0      1    0
## ACH-000027   1      0    0
## ACH-000028   0      0    1
## ACH-000029   0      1    0
## ACH-000030   0      0    1
## ACH-000031   1      0    0
## ACH-000033   1      0    0
## ACH-000035   1      0    0
## ACH-000039   1      0    0
## ACH-000040   1      0    0
## ACH-000041   1      0    0
## ACH-000042   1      0    0
## ACH-000043   1      0    0
## ACH-000044   1      0    0
## ACH-000045   1      0    0
## ACH-000046   1      0    0
## ACH-000048   1      0    0
## ACH-000050   0      1    0
## ACH-000051   1      0    0
## ACH-000052   1      0    0
## ACH-000054   1      0    0
## ACH-000055   1      0    0
## ACH-000056   1      0    0
## ACH-000059   1      0    0
## ACH-000060   1      0    0
## ACH-000062   0      1    0
## ACH-000065   1      0    0
## ACH-000066   1      0    0
## ACH-000067   1      0    0
## ACH-000070   1      0    0
## ACH-000073   1      0    0
## ACH-000075   1      0    0
## ACH-000078   1      0    0
## ACH-000082   1      0    0
## ACH-000085   1      0    0
## ACH-000087   1      0    0
## ACH-000089   1      0    0
## ACH-000090   0      0    1
## ACH-000091   1      0    0
## ACH-000092   1      0    0
## ACH-000093   1      0    0
## ACH-000094   1      0    0
## ACH-000096   1      0    0
## ACH-000097   0      1    0
## ACH-000098   1      0    0
## ACH-000100   1      0    0
## ACH-000102   1      0    0
## ACH-000103   1      0    0
## ACH-000105   1      0    0
## ACH-000107   1      0    0
## ACH-000108   0      1    0
## ACH-000109   0      1    0
## ACH-000111   1      0    0
## ACH-000113   1      0    0
## ACH-000114   1      0    0
## ACH-000115   1      0    0
## ACH-000116   1      0    0
## ACH-000117   1      0    0
## ACH-000118   0      1    0
## ACH-000121   1      0    0
## ACH-000123   1      0    0
## ACH-000124   1      0    0
## ACH-000125   1      0    0
## ACH-000126   0      1    0
## ACH-000127   0      1    0
## ACH-000129   1      0    0
## ACH-000131   1      0    0
## ACH-000132   0      1    0
## ACH-000133   1      0    0
## ACH-000135   1      0    0
## ACH-000136   1      0    0
## ACH-000137   1      0    0
## ACH-000138   1      0    0
## ACH-000139   1      0    0
## ACH-000140   1      0    0
## ACH-000142   1      0    0
## ACH-000144   0      1    0
## ACH-000145   1      0    0
## ACH-000146   0      1    0
## ACH-000147   1      0    0
## ACH-000148   1      0    0
## ACH-000149   1      0    0
## ACH-000150   1      0    0
## ACH-000152   1      0    0
## ACH-000153   0      1    0
## ACH-000155   1      0    0
## ACH-000157   0      0    1
## ACH-000158   0      1    0
## ACH-000159   0      1    0
## ACH-000161   1      0    0
## ACH-000163   1      0    0
## ACH-000164   1      0    0
## ACH-000166   0      1    0
## ACH-000167   0      1    0
## ACH-000168   0      1    0
## ACH-000169   0      1    0
## ACH-000171   1      0    0
## ACH-000172   1      0    0
## ACH-000174   1      0    0
## ACH-000176   1      0    0
## ACH-000177   0      1    0
## ACH-000178   1      0    0
## ACH-000179   0      1    0
## ACH-000181   0      1    0
## ACH-000183   0      1    0
## ACH-000186   0      1    0
## ACH-000187   1      0    0
## ACH-000188   1      0    0
## ACH-000189   0      1    0
## ACH-000191   1      0    0
## ACH-000192   0      1    0
## ACH-000193   1      0    0
## ACH-000194   1      0    0
## ACH-000196   0      0    1
## ACH-000197   0      1    0
## ACH-000200   0      1    0
## ACH-000201   1      0    0
## ACH-000202   0      1    0
## ACH-000203   0      1    0
## ACH-000204   0      1    0
## ACH-000205   0      1    0
## ACH-000207   0      1    0
## ACH-000210   0      1    0
## ACH-000211   0      1    0
## ACH-000212   1      0    0
## ACH-000213   0      1    0
## ACH-000217   0      1    0
## ACH-000219   0      0    1
## ACH-000221   0      1    0
## ACH-000222   0      1    0
## ACH-000223   0      1    0
## ACH-000227   0      1    0
## ACH-000228   1      0    0
## ACH-000229   1      0    0
## ACH-000231   0      1    0
## ACH-000232   0      1    0
## ACH-000234   1      0    0
## ACH-000235   0      1    0
## ACH-000236   0      1    0
## ACH-000237   0      1    0
## ACH-000238   0      1    0
## ACH-000239   0      1    0
## ACH-000240   1      0    0
## ACH-000242   1      0    0
## ACH-000244   1      0    0
## ACH-000246   0      1    0
## ACH-000247   0      1    0
## ACH-000248   0      0    1
## ACH-000249   1      0    0
## ACH-000250   0      1    0
## ACH-000252   0      1    0
## ACH-000253   0      1    0
## ACH-000255   0      1    0
## ACH-000256   1      0    0
## ACH-000257   0      1    0
## ACH-000258   0      1    0
## ACH-000259   0      1    0
## ACH-000260   1      0    0
## ACH-000261   0      1    0
## ACH-000263   0      1    0
## ACH-000264   0      1    0
## ACH-000265   0      1    0
## ACH-000269   0      1    0
## ACH-000270   0      1    0
## ACH-000271   1      0    0
## ACH-000272   1      0    0
## ACH-000273   1      0    0
## ACH-000275   1      0    0
## ACH-000276   0      1    0
## ACH-000277   0      1    0
## ACH-000278   0      1    0
## ACH-000280   0      1    0
## ACH-000281   0      1    0
## ACH-000282   0      1    0
## ACH-000285   0      1    0
## ACH-000286   0      1    0
## ACH-000288   1      0    0
## ACH-000290   0      1    0
## ACH-000291   1      0    0
## ACH-000292   0      1    0
## ACH-000293   1      0    0
## ACH-000294   0      1    0
## ACH-000296   0      0    1
## ACH-000297   0      1    0
## ACH-000298   0      1    0
## ACH-000300   1      0    0
## ACH-000301   0      1    0
## ACH-000302   0      1    0
## ACH-000303   0      1    0
## ACH-000304   0      0    1
## ACH-000306   1      0    0
## ACH-000307   0      1    0
## ACH-000308   0      1    0
## ACH-000310   1      0    0
## ACH-000311   0      1    0
## ACH-000312   0      1    0
## ACH-000313   0      1    0
## ACH-000314   0      0    1
## ACH-000315   0      1    0
## ACH-000317   0      1    0
## ACH-000318   0      1    0
## ACH-000320   0      1    0
## ACH-000322   0      1    0
## ACH-000323   1      0    0
## ACH-000324   0      1    0
## ACH-000325   0      1    0
## ACH-000327   1      0    0
## ACH-000329   1      0    0
## ACH-000330   0      1    0
## ACH-000332   0      1    0
## ACH-000333   1      0    0
## ACH-000334   0      1    0
## ACH-000335   1      0    0
## ACH-000336   1      0    0
## ACH-000338   0      1    0
## ACH-000341   0      1    0
## ACH-000343   0      1    0
## ACH-000344   0      1    0
## ACH-000345   0      1    0
## ACH-000347   0      0    1
## ACH-000348   0      1    0
## ACH-000349   0      1    0
## ACH-000350   0      0    1
## ACH-000351   0      1    0
## ACH-000352   0      1    0
## ACH-000353   0      0    1
## ACH-000354   0      1    0
## ACH-000355   0      1    0
## ACH-000356   0      1    0
## ACH-000358   0      1    0
## ACH-000359   1      0    0
## ACH-000360   0      1    0
## ACH-000361   1      0    0
## ACH-000362   0      1    0
## ACH-000363   0      1    0
## ACH-000364   0      1    0
## ACH-000365   0      1    0
## ACH-000366   0      1    0
## ACH-000367   1      0    0
## ACH-000368   0      1    0
## ACH-000373   0      1    0
## ACH-000374   1      0    0
## ACH-000375   0      1    0
## ACH-000376   0      1    0
## ACH-000378   0      1    0
## ACH-000379   0      1    0
## ACH-000380   0      1    0
## ACH-000381   0      0    1
## ACH-000382   0      1    0
## ACH-000383   0      1    0
## ACH-000384   0      1    0
## ACH-000386   0      1    0
## ACH-000388   0      1    0
## ACH-000389   0      1    0
## ACH-000390   0      1    0
## ACH-000391   0      1    0
## ACH-000392   0      1    0
## ACH-000393   0      1    0
## ACH-000394   0      0    1
## ACH-000395   0      0    1
## ACH-000396   0      1    0
## ACH-000397   0      1    0
## ACH-000399   0      1    0
## ACH-000400   0      1    0
## ACH-000401   0      1    0
## ACH-000403   1      0    0
## ACH-000404   0      1    0
## ACH-000406   0      1    0
## ACH-000407   0      1    0
## ACH-000409   0      1    0
## ACH-000410   0      1    0
## ACH-000411   1      0    0
## ACH-000412   0      1    0
## ACH-000414   0      0    1
## ACH-000415   1      0    0
## ACH-000416   0      0    1
## ACH-000417   0      1    0
## ACH-000418   1      0    0
## ACH-000419   0      0    1
## ACH-000420   0      1    0
## ACH-000421   0      1    0
## ACH-000422   0      1    0
## ACH-000423   0      1    0
## ACH-000424   0      1    0
## ACH-000427   0      1    0
## ACH-000429   0      0    1
## ACH-000430   0      1    0
## ACH-000431   0      0    1
## ACH-000433   1      0    0
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## ACH-001530   0      0    1
## ACH-001532   1      0    0
## ACH-001536   0      0    1
## ACH-001538   0      1    0
## ACH-001539   0      0    1
## ACH-001540   0      1    0
## ACH-001541   0      1    0
## ACH-001542   0      0    1
## ACH-001543   0      1    0
## ACH-001548   1      0    0
## ACH-001549   0      0    1
## ACH-001550   0      0    1
## ACH-001551   0      0    1
## ACH-001552   0      0    1
## ACH-001554   1      0    0
## ACH-001555   1      0    0
## ACH-001556   1      0    0
## ACH-001557   1      0    0
## ACH-001558   1      0    0
## ACH-001559   1      0    0
## ACH-001560   1      0    0
## ACH-001561   1      0    0
## ACH-001562   1      0    0
## ACH-001563   0      0    1
## ACH-001566   0      0    1
## ACH-001567   0      0    1
## ACH-001568   0      0    1
## ACH-001569   0      0    1
## ACH-001570   0      0    1
## ACH-001573   1      0    0
## ACH-001574   1      0    0
## ACH-001577   1      0    0
## ACH-001578   0      1    0
## ACH-001603   0      1    0
## ACH-001605   0      1    0
## ACH-001607   0      1    0
## ACH-001608   0      0    1
## ACH-001609   0      1    0
## ACH-001610   0      0    1
## ACH-001611   0      1    0
## ACH-001613   1      0    0
## ACH-001616   1      0    0
## ACH-001617   1      0    0
## ACH-001618   1      0    0
## ACH-001619   0      1    0
## ACH-001622   0      1    0
## ACH-001623   0      0    1
## ACH-001624   0      1    0
## ACH-001625   0      0    1
## ACH-001626   0      1    0
## ACH-001627   1      0    0
## ACH-001628   1      0    0
## ACH-001630   0      1    0
## ACH-001632   1      0    0
## ACH-001634   1      0    0
## ACH-001636   1      0    0
## ACH-001638   0      0    1
## ACH-001642   0      1    0
## ACH-001645   0      0    1
## ACH-001647   0      1    0
## ACH-001648   1      0    0
## ACH-001649   1      0    0
## ACH-001650   0      0    1
## ACH-001651   1      0    0
## ACH-001652   0      1    0
## ACH-001653   0      0    1
## ACH-001654   1      0    0
## ACH-001655   0      1    0
## ACH-001656   0      1    0
## ACH-001664   0      0    1
## ACH-001668   1      0    0
## ACH-001670   0      1    0
## ACH-001673   0      1    0
## ACH-001674   0      0    1
## ACH-001677   1      0    0
## ACH-001685   0      1    0
## ACH-001687   0      1    0
## ACH-001688   0      1    0
## ACH-001690   1      0    0
## ACH-001692   1      0    0
## ACH-001694   0      0    1
## ACH-001698   1      0    0
## ACH-001699   0      1    0
## ACH-001702   1      0    0
## ACH-001703   1      0    0
## ACH-001709   0      0    1
## ACH-001711   1      0    0
## ACH-001719   0      0    1
## ACH-001740   0      1    0
## ACH-001765   1      0    0
## ACH-001786   0      0    1
## ACH-001794   1      0    0
## ACH-001807   1      0    0
## ACH-001814   1      0    0
## ACH-001818   1      0    0
## ACH-001819   0      1    0
## ACH-001820   0      1    0
## ACH-001850   0      1    0
## ACH-001861   0      1    0
## ACH-001961   1      0    0
## ACH-001991   0      0    1
## ACH-002011   1      0    0
## ACH-002015   1      0    0
## ACH-002016   1      0    0
## ACH-002017   0      1    0
## ACH-002018   1      0    0
## ACH-002019   0      1    0
## ACH-002022   0      0    1
## ACH-002023   0      1    0
## ACH-002024   0      0    1
## ACH-002025   0      1    0
## ACH-002026   0      0    1
## ACH-002027   0      0    1
## ACH-002029   0      0    1
## ACH-002038   0      1    0
## ACH-002039   0      1    0
## ACH-002041   0      0    1
## ACH-002042   0      1    0
## ACH-002044   0      1    0
## ACH-002045   0      0    1
## ACH-002046   0      1    0
## ACH-002059   0      0    1
## ACH-002062   0      0    1
## ACH-002065   0      1    0
## ACH-002066   0      1    0
## ACH-002067   0      1    0
## ACH-002069   0      1    0
## ACH-002446   0      1    0
## ACH-002508   0      0    1
## ACH-002509   0      0    1
## ACH-002510   0      0    1
## ACH-002511   1      0    0
## attr(,"assign")
## [1] 1 1 1
## attr(,"contrasts")
## attr(,"contrasts")$Mutation_count
## [1] "contr.treatment"

##         MvsL  HvsM  HvsL
## Down     908   902  3964
## NotSig 19843 20543 13636
## Up      1461   767  4612

##                     logFC       AveExpr         t      P.Value    adj.P.Val
## ENSG00000224271  2.510643 -3.3884166903 10.473678 1.882903e-24 4.182304e-20
## ENSG00000221867  3.845289  0.5383173374  9.534024 1.067607e-20 1.185684e-16
## ENSG00000197172  3.699421  0.0591463471  9.451578 2.208600e-20 1.635247e-16
## ENSG00000279712  2.071435 -4.1058346623  9.385180 3.951306e-20 2.194160e-16
## ENSG00000132274 -2.491091  1.6510253853 -9.163649 2.685327e-19 1.192930e-15
## ENSG00000154175 -2.179250 -0.0008381123 -9.032198 8.223786e-19 3.044446e-15
## ENSG00000172638 -1.789188  2.2265786145 -8.930388 1.938837e-18 5.383182e-15
## ENSG00000268606  3.451761 -1.4222605719  8.950203 1.641822e-18 5.209735e-15
## ENSG00000282944  1.910403 -4.9031569178  8.820372 4.853819e-18 1.197923e-14
## ENSG00000205634  1.794872 -4.7852617419  8.800423 5.726758e-18 1.272027e-14
##                        B
## ENSG00000224271 44.15356
## ENSG00000221867 36.06562
## ENSG00000197172 35.33394
## ENSG00000279712 34.58861
## ENSG00000132274 33.06661
## ENSG00000154175 31.89268
## ENSG00000172638 31.14717
## ENSG00000268606 31.11845
## ENSG00000282944 29.96770
## ENSG00000205634 29.81070

##         MvsL  HvsM  HvsL
## Down       1    20   875
## NotSig 22203 22175 20411
## Up         8    17   926

## Warning in makeAnno(x, anno): No gene annotation provided.
##      query significant      p_value term_size query_size intersection_size
## 1  query_1        TRUE 9.837452e-30      4053       1083               371
## 2  query_1        TRUE 4.349511e-29      1534       1083               193
## 3  query_1        TRUE 5.166588e-29      5997       1083               487
## 4  query_1        TRUE 2.427372e-28      7322       1083               560
## 5  query_1        TRUE 2.844991e-28      4727       1083               409
## 6  query_1        TRUE 3.384786e-28      2713       1083               278
## 7  query_1        TRUE 6.338640e-28      2956       1083               294
## 8  query_1        TRUE 1.002168e-27      6553       1083               515
## 9  query_1        TRUE 9.683175e-27      1793       1083               208
## 10 query_1        TRUE 1.670193e-25      1145       1083               154
##    precision     recall    term_id source
## 1  0.3425669 0.09153713 GO:0048731  GO:BP
## 2  0.1782087 0.12581486 GO:0016477  GO:BP
## 3  0.4496768 0.08120727 GO:0048856  GO:BP
## 4  0.5170822 0.07648184 GO:0032501  GO:BP
## 5  0.3776547 0.08652422 GO:0007275  GO:BP
## 6  0.2566944 0.10246959 GO:0009653  GO:BP
## 7  0.2714681 0.09945873 GO:0051239  GO:BP
## 8  0.4755309 0.07858996 GO:0032502  GO:BP
## 9  0.1920591 0.11600669 GO:0048870  GO:BP
## 10 0.1421976 0.13449782 GO:0072359  GO:BP
##                                         term_name effective_domain_size
## 1                              system development                 21026
## 2                                  cell migration                 21026
## 3                anatomical structure development                 21026
## 4                multicellular organismal process                 21026
## 5              multicellular organism development                 21026
## 6              anatomical structure morphogenesis                 21026
## 7  regulation of multicellular organismal process                 21026
## 8                           developmental process                 21026
## 9                                   cell motility                 21026
## 10                 circulatory system development                 21026
##    source_order      parents
## 1         12821 GO:00072....
## 2          5204   GO:0048870
## 3         12931   GO:0032502
## 4          7557   GO:0008150
## 5          2788 GO:00325....
## 6          3557 GO:00325....
## 7         13407 GO:00325....
## 8          7558   GO:0008150
## 9         12944   GO:0009987
## 10        17136   GO:0048731

Contrasts MvsL, HvsM, HvsL were defined. After filtering 18,306 genes remained. TREAT results: MvsL -> 2 overexpressed; HvsM -> 18 under, 12 over; HvsL -> 698 under, 587 over. GO results for HvsL suggest underexpression of ECM, angiogenesis and cell adhesion related genes in high vs low mutation loads.

Back to analysis

Combination

##            Metastasis.High Metastasis.Low Metastasis.Medium Primary.High
## ACH-000001               0              0                 1            0
## ACH-000002               0              0                 0            0
## ACH-000006               0              0                 0            0
## ACH-000007               0              0                 0            0
## ACH-000009               0              0                 0            0
## ACH-000011               0              0                 1            0
## ACH-000012               0              0                 0            0
## ACH-000013               0              1                 0            0
## ACH-000014               1              0                 0            0
## ACH-000015               0              0                 0            0
## ACH-000016               0              1                 0            0
## ACH-000017               0              0                 1            0
## ACH-000018               0              0                 0            0
## ACH-000019               1              0                 0            0
## ACH-000021               0              0                 1            0
## ACH-000022               0              1                 0            0
## ACH-000023               0              0                 1            0
## ACH-000024               0              0                 0            1
## ACH-000026               0              0                 1            0
## ACH-000027               0              0                 0            0
## ACH-000028               1              0                 0            0
## ACH-000029               0              0                 0            0
## ACH-000030               0              0                 0            1
## ACH-000031               0              0                 0            0
## ACH-000033               0              1                 0            0
## ACH-000035               0              1                 0            0
## ACH-000039               0              1                 0            0
## ACH-000040               0              0                 0            0
## ACH-000041               0              0                 0            0
## ACH-000042               0              0                 0            0
## ACH-000043               0              1                 0            0
## ACH-000044               0              1                 0            0
## ACH-000045               0              0                 0            0
## ACH-000046               0              1                 0            0
## ACH-000048               0              0                 0            0
## ACH-000050               0              0                 1            0
## ACH-000051               0              0                 0            0
## ACH-000052               0              0                 0            0
## ACH-000054               0              1                 0            0
## ACH-000055               0              1                 0            0
## ACH-000056               0              1                 0            0
## ACH-000059               0              0                 0            0
## ACH-000060               0              0                 0            0
## ACH-000062               0              0                 0            0
## ACH-000065               0              0                 0            0
## ACH-000066               0              1                 0            0
## ACH-000067               0              0                 0            0
## ACH-000070               0              0                 0            0
## ACH-000073               0              0                 0            0
## ACH-000075               0              0                 0            0
## ACH-000078               0              1                 0            0
## ACH-000082               0              0                 0            0
## ACH-000085               0              0                 0            0
## ACH-000087               0              0                 0            0
## ACH-000089               0              1                 0            0
## ACH-000090               1              0                 0            0
## ACH-000091               0              1                 0            0
## ACH-000092               0              1                 0            0
## ACH-000093               0              0                 0            0
## ACH-000094               0              1                 0            0
## ACH-000096               0              0                 0            0
## ACH-000097               0              0                 1            0
## ACH-000098               0              0                 0            0
## ACH-000100               0              1                 0            0
## ACH-000102               0              0                 0            0
## ACH-000103               0              1                 0            0
## ACH-000105               0              0                 0            0
## ACH-000107               0              0                 0            0
## ACH-000108               0              0                 1            0
## ACH-000109               0              0                 0            0
## ACH-000111               0              0                 0            0
## ACH-000113               0              0                 0            0
## ACH-000114               0              1                 0            0
## ACH-000115               0              1                 0            0
## ACH-000116               0              1                 0            0
## ACH-000117               0              1                 0            0
## ACH-000118               0              0                 1            0
## ACH-000121               0              1                 0            0
## ACH-000123               0              0                 0            0
## ACH-000124               0              0                 0            0
## ACH-000125               0              1                 0            0
## ACH-000126               0              0                 0            0
## ACH-000127               0              0                 0            0
## ACH-000129               0              1                 0            0
## ACH-000131               0              0                 0            0
## ACH-000132               0              0                 0            0
## ACH-000133               0              0                 0            0
## ACH-000135               0              0                 0            0
## ACH-000136               0              0                 0            0
## ACH-000137               0              0                 0            0
## ACH-000138               0              1                 0            0
## ACH-000139               0              0                 0            0
## ACH-000140               0              1                 0            0
## ACH-000142               0              0                 0            0
## ACH-000144               0              0                 1            0
## ACH-000145               0              0                 0            0
## ACH-000146               0              0                 0            0
## ACH-000147               0              1                 0            0
## ACH-000148               0              0                 0            0
## ACH-000149               0              1                 0            0
## ACH-000150               0              0                 0            0
## ACH-000152               0              0                 0            0
## ACH-000153               0              0                 1            0
## ACH-000155               0              0                 0            0
## ACH-000157               0              0                 0            1
## ACH-000158               0              0                 0            0
## ACH-000159               0              0                 0            0
## ACH-000161               0              1                 0            0
## ACH-000163               0              0                 0            0
## ACH-000164               0              0                 0            0
## ACH-000166               0              0                 0            0
## ACH-000167               0              0                 1            0
## ACH-000168               0              0                 0            0
## ACH-000169               0              0                 0            0
## ACH-000171               0              0                 0            0
## ACH-000172               0              1                 0            0
## ACH-000174               0              0                 0            0
## ACH-000176               0              0                 0            0
## ACH-000177               0              0                 1            0
## ACH-000178               0              1                 0            0
## ACH-000179               0              0                 1            0
## ACH-000181               0              0                 0            0
## ACH-000183               0              0                 0            0
## ACH-000186               0              0                 0            0
## ACH-000187               0              0                 0            0
## ACH-000188               0              0                 0            0
## ACH-000189               0              0                 0            0
## ACH-000191               0              1                 0            0
## ACH-000192               0              0                 0            0
## ACH-000193               0              0                 0            0
## ACH-000194               0              0                 0            0
## ACH-000196               0              0                 0            1
## ACH-000197               0              0                 0            0
## ACH-000200               0              0                 0            0
## ACH-000201               0              0                 0            0
## ACH-000202               0              0                 0            0
## ACH-000203               0              0                 1            0
## ACH-000204               0              0                 0            0
## ACH-000205               0              0                 1            0
## ACH-000207               0              0                 1            0
## ACH-000210               0              0                 1            0
## ACH-000211               0              0                 0            0
## ACH-000212               0              1                 0            0
## ACH-000213               0              0                 1            0
## ACH-000217               0              0                 0            0
## ACH-000219               0              0                 0            1
## ACH-000221               0              0                 0            0
## ACH-000222               0              0                 1            0
## ACH-000223               0              0                 0            0
## ACH-000227               0              0                 1            0
## ACH-000228               0              0                 0            0
## ACH-000229               0              0                 0            0
## ACH-000231               0              0                 0            0
## ACH-000232               0              0                 0            0
## ACH-000234               0              0                 0            0
## ACH-000235               0              0                 0            0
## ACH-000236               0              0                 0            0
## ACH-000237               0              0                 0            0
## ACH-000238               0              0                 0            0
## ACH-000239               0              0                 1            0
## ACH-000240               0              0                 0            0
## ACH-000242               0              0                 0            0
## ACH-000244               0              0                 0            0
## ACH-000246               0              0                 1            0
## ACH-000247               0              0                 1            0
## ACH-000248               1              0                 0            0
## ACH-000249               0              0                 0            0
## ACH-000250               0              0                 0            0
## ACH-000252               0              0                 0            0
## ACH-000253               0              0                 1            0
## ACH-000255               0              0                 1            0
## ACH-000256               0              1                 0            0
## ACH-000257               0              0                 1            0
## ACH-000258               0              0                 1            0
## ACH-000259               0              0                 0            0
## ACH-000260               0              1                 0            0
## ACH-000261               0              0                 1            0
## ACH-000263               0              0                 0            0
## ACH-000264               0              0                 1            0
## ACH-000265               0              0                 1            0
## ACH-000269               0              0                 0            0
## ACH-000270               0              0                 0            0
## ACH-000271               0              1                 0            0
## ACH-000272               0              0                 0            0
## ACH-000273               0              0                 0            0
## ACH-000275               0              1                 0            0
## ACH-000276               0              0                 0            0
## ACH-000277               0              0                 0            0
## ACH-000278               0              0                 1            0
## ACH-000280               0              0                 0            0
## ACH-000281               0              0                 0            0
## ACH-000282               0              0                 1            0
## ACH-000285               0              0                 0            0
## ACH-000286               0              0                 0            0
## ACH-000288               0              0                 0            0
## ACH-000290               0              0                 1            0
## ACH-000291               0              1                 0            0
## ACH-000292               0              0                 1            0
## ACH-000293               0              0                 0            0
## ACH-000294               0              0                 0            0
## ACH-000296               1              0                 0            0
## ACH-000297               0              0                 1            0
## ACH-000298               0              0                 1            0
## ACH-000300               0              1                 0            0
## ACH-000301               0              0                 0            0
## ACH-000302               0              0                 0            0
## ACH-000303               0              0                 1            0
## ACH-000304               1              0                 0            0
## ACH-000306               0              0                 0            0
## ACH-000307               0              0                 1            0
## ACH-000308               0              0                 1            0
## ACH-000310               0              1                 0            0
## ACH-000311               0              0                 1            0
## ACH-000312               0              0                 1            0
## ACH-000313               0              0                 0            0
## ACH-000314               0              0                 0            1
## ACH-000315               0              0                 1            0
## ACH-000317               0              0                 0            0
## ACH-000318               0              0                 0            0
## ACH-000320               0              0                 0            0
## ACH-000322               0              0                 1            0
## ACH-000323               0              0                 0            0
## ACH-000324               0              0                 0            0
## ACH-000325               0              0                 1            0
## ACH-000327               0              0                 0            0
## ACH-000329               0              0                 0            0
## ACH-000330               0              0                 1            0
## ACH-000332               0              0                 1            0
## ACH-000333               0              0                 0            0
## ACH-000334               0              0                 1            0
## ACH-000335               0              1                 0            0
## ACH-000336               0              0                 0            0
## ACH-000338               0              0                 0            0
## ACH-000341               0              0                 1            0
## ACH-000343               0              0                 0            0
## ACH-000344               0              0                 1            0
## ACH-000345               0              0                 1            0
## ACH-000347               0              0                 0            1
## ACH-000348               0              0                 1            0
## ACH-000349               0              0                 0            0
## ACH-000350               1              0                 0            0
## ACH-000351               0              0                 1            0
## ACH-000352               0              0                 1            0
## ACH-000353               0              0                 0            1
## ACH-000354               0              0                 1            0
## ACH-000355               0              0                 1            0
## ACH-000356               0              0                 1            0
## ACH-000358               0              0                 1            0
## ACH-000359               0              0                 0            0
## ACH-000360               0              0                 1            0
## ACH-000361               0              1                 0            0
## ACH-000362               0              0                 0            0
## ACH-000363               0              0                 0            0
## ACH-000364               0              0                 0            0
## ACH-000365               0              0                 1            0
## ACH-000366               0              0                 1            0
## ACH-000367               0              1                 0            0
## ACH-000368               0              0                 0            0
## ACH-000373               0              0                 0            0
## ACH-000374               0              0                 0            0
## ACH-000375               0              0                 0            0
## ACH-000376               0              0                 0            0
## ACH-000378               0              0                 1            0
## ACH-000379               0              0                 1            0
## ACH-000380               0              0                 0            0
## ACH-000381               1              0                 0            0
## ACH-000382               0              0                 1            0
## ACH-000383               0              0                 0            0
## ACH-000384               0              0                 0            0
## ACH-000386               0              0                 0            0
## ACH-000388               0              0                 1            0
## ACH-000389               0              0                 0            0
## ACH-000390               0              0                 0            0
## ACH-000391               0              0                 1            0
## ACH-000392               0              0                 1            0
## ACH-000393               0              0                 0            0
## ACH-000394               1              0                 0            0
## ACH-000395               0              0                 0            1
## ACH-000396               0              0                 0            0
## ACH-000397               0              0                 0            0
## ACH-000399               0              0                 1            0
## ACH-000400               0              0                 1            0
## ACH-000401               0              0                 1            0
## ACH-000403               0              1                 0            0
## ACH-000404               0              0                 0            0
## ACH-000406               0              0                 1            0
## ACH-000407               0              0                 0            0
## ACH-000409               0              0                 1            0
## ACH-000410               0              0                 0            0
## ACH-000411               0              0                 0            0
## ACH-000412               0              0                 0            0
## ACH-000414               1              0                 0            0
## ACH-000415               0              0                 0            0
## ACH-000416               1              0                 0            0
## ACH-000417               0              0                 0            0
## ACH-000418               0              0                 0            0
## ACH-000419               0              0                 0            1
## ACH-000420               0              0                 0            0
## ACH-000421               0              0                 0            0
## ACH-000422               0              0                 0            0
## ACH-000423               0              0                 1            0
## ACH-000424               0              0                 0            0
## ACH-000427               0              0                 1            0
## ACH-000429               0              0                 0            1
## ACH-000430               0              0                 0            0
## ACH-000431               1              0                 0            0
## ACH-000433               0              1                 0            0
## ACH-000434               1              0                 0            0
## ACH-000435               0              1                 0            0
## ACH-000437               0              0                 0            0
## ACH-000438               0              0                 0            0
## ACH-000441               0              0                 1            0
## ACH-000442               0              0                 0            0
## ACH-000443               0              0                 0            0
## ACH-000444               1              0                 0            0
## ACH-000445               0              0                 0            0
## ACH-000446               0              0                 1            0
## ACH-000447               0              0                 0            0
## ACH-000448               1              0                 0            0
## ACH-000449               0              0                 0            0
## ACH-000450               0              0                 0            0
## ACH-000451               0              0                 0            0
## ACH-000453               0              0                 0            0
## ACH-000454               0              0                 1            0
## ACH-000456               0              0                 0            0
## ACH-000457               0              0                 1            0
## ACH-000458               0              0                 1            0
## ACH-000459               0              0                 0            0
## ACH-000460               0              0                 1            0
## ACH-000463               1              0                 0            0
## ACH-000464               0              0                 0            0
## ACH-000465               0              0                 1            0
## ACH-000466               0              0                 1            0
## ACH-000468               0              0                 0            0
## ACH-000469               0              0                 0            0
## ACH-000470               0              0                 0            1
## ACH-000472               1              0                 0            0
## ACH-000473               0              0                 0            1
## ACH-000475               0              0                 0            1
## ACH-000476               0              0                 0            0
## ACH-000477               0              0                 1            0
## ACH-000478               0              0                 0            0
## ACH-000479               0              0                 0            0
## ACH-000480               0              0                 0            0
## ACH-000481               0              0                 0            1
## ACH-000482               0              0                 0            0
## ACH-000483               0              0                 0            0
## ACH-000484               0              0                 0            0
## ACH-000485               0              0                 1            0
## ACH-000487               0              0                 1            0
## ACH-000488               0              0                 0            1
## ACH-000489               0              0                 0            0
## ACH-000490               0              0                 1            0
## ACH-000491               1              0                 0            0
## ACH-000493               0              0                 0            0
## ACH-000495               0              0                 0            0
## ACH-000496               0              0                 1            0
## ACH-000501               0              0                 0            1
## ACH-000502               0              1                 0            0
## ACH-000503               0              0                 0            0
## ACH-000504               0              0                 0            0
## ACH-000505               0              0                 0            0
## ACH-000506               0              0                 1            0
## ACH-000507               1              0                 0            0
## ACH-000508               1              0                 0            0
## ACH-000510               1              0                 0            0
## ACH-000511               1              0                 0            0
## ACH-000514               1              0                 0            0
## ACH-000515               1              0                 0            0
## ACH-000517               0              0                 1            0
## ACH-000518               0              0                 0            0
## ACH-000520               0              0                 1            0
## ACH-000521               1              0                 0            0
## ACH-000522               0              0                 0            0
## ACH-000523               1              0                 0            0
## ACH-000524               0              0                 1            0
## ACH-000525               0              0                 1            0
## ACH-000526               0              0                 0            0
## ACH-000527               1              0                 0            0
## ACH-000528               1              0                 0            0
## ACH-000530               0              0                 0            0
## ACH-000532               0              0                 1            0
## ACH-000534               0              0                 1            0
## ACH-000535               0              0                 0            0
## ACH-000536               0              0                 0            1
## ACH-000538               0              0                 0            0
## ACH-000539               0              0                 0            0
## ACH-000541               0              0                 0            1
## ACH-000542               0              0                 1            0
## ACH-000544               0              0                 0            0
## ACH-000545               0              0                 0            1
## ACH-000546               1              0                 0            0
## ACH-000547               0              0                 0            0
## ACH-000548               0              0                 0            1
## ACH-000550               0              0                 0            1
## ACH-000551               1              0                 0            0
## ACH-000552               0              0                 0            1
## ACH-000553               0              0                 0            1
## ACH-000554               0              0                 0            1
## ACH-000555               0              0                 0            0
## ACH-000557               0              0                 0            0
## ACH-000558               0              0                 0            0
## ACH-000559               0              0                 0            1
## ACH-000561               1              0                 0            0
## ACH-000562               0              0                 1            0
## ACH-000563               1              0                 0            0
## ACH-000564               0              0                 0            1
## ACH-000565               0              0                 0            1
## ACH-000566               0              0                 0            0
## ACH-000568               0              0                 0            0
## ACH-000569               0              0                 0            0
## ACH-000570               0              0                 0            1
## ACH-000571               0              0                 0            0
## ACH-000572               0              0                 0            0
## ACH-000573               0              0                 1            0
## ACH-000574               0              0                 0            1
## ACH-000576               0              0                 0            1
## ACH-000577               0              0                 1            0
## ACH-000578               0              0                 0            0
## ACH-000579               0              0                 0            1
## ACH-000580               0              0                 0            0
## ACH-000581               0              0                 1            0
## ACH-000582               1              0                 0            0
## ACH-000584               0              0                 0            1
## ACH-000585               0              0                 0            1
## ACH-000586               1              0                 0            0
## ACH-000587               0              0                 0            0
## ACH-000588               0              0                 0            1
## ACH-000589               1              0                 0            0
## ACH-000590               0              0                 0            1
## ACH-000593               0              0                 0            0
## ACH-000594               1              0                 0            0
## ACH-000595               0              0                 0            1
## ACH-000596               0              0                 0            1
## ACH-000598               0              0                 0            1
## ACH-000599               0              0                 0            0
## ACH-000600               0              0                 0            0
## ACH-000601               0              0                 0            0
## ACH-000603               1              0                 0            0
## ACH-000606               0              0                 0            0
## ACH-000607               0              0                 0            1
## ACH-000608               0              0                 0            0
## ACH-000609               0              0                 0            0
## ACH-000610               0              0                 0            1
## ACH-000611               1              0                 0            0
## ACH-000613               0              0                 0            0
## ACH-000614               1              0                 0            0
## ACH-000616               1              0                 0            0
## ACH-000617               0              0                 1            0
## ACH-000619               0              0                 0            0
## ACH-000620               0              0                 0            1
## ACH-000621               1              0                 0            0
## ACH-000622               0              0                 0            1
## ACH-000623               0              0                 0            0
## ACH-000624               0              0                 0            0
## ACH-000625               0              0                 0            0
## ACH-000627               1              0                 0            0
## ACH-000628               0              0                 0            1
## ACH-000631               0              0                 0            1
## ACH-000632               1              0                 0            0
## ACH-000633               0              0                 0            1
## ACH-000635               1              0                 0            0
## ACH-000637               0              0                 0            1
## ACH-000638               1              0                 0            0
## ACH-000639               1              0                 0            0
## ACH-000640               0              0                 0            1
## ACH-000643               0              0                 0            1
## ACH-000644               0              0                 0            0
## ACH-000645               0              0                 0            0
## ACH-000646               0              0                 0            1
## ACH-000647               0              0                 0            1
## ACH-000648               0              0                 1            0
## ACH-000649               0              0                 0            1
## ACH-000650               1              0                 0            0
## ACH-000651               1              0                 0            0
## ACH-000652               1              0                 0            0
## ACH-000653               0              0                 0            0
## ACH-000655               0              0                 0            0
## ACH-000656               1              0                 0            0
## ACH-000657               0              0                 0            1
## ACH-000658               0              0                 0            1
## ACH-000659               1              0                 0            0
## ACH-000660               0              0                 0            0
## ACH-000662               1              0                 0            0
## ACH-000663               1              0                 0            0
## ACH-000665               1              0                 0            0
## ACH-000666               1              0                 0            0
## ACH-000667               0              0                 0            1
## ACH-000668               0              0                 0            0
## ACH-000669               0              0                 0            1
## ACH-000670               1              0                 0            0
## ACH-000672               1              0                 0            0
## ACH-000674               1              0                 0            0
## ACH-000675               0              0                 0            1
## ACH-000677               0              0                 0            0
## ACH-000678               1              0                 0            0
## ACH-000679               0              0                 0            1
## ACH-000680               0              0                 0            1
## ACH-000681               0              0                 0            1
## ACH-000683               1              0                 0            0
## ACH-000684               0              0                 0            0
## ACH-000685               0              0                 1            0
## ACH-000686               0              0                 0            0
## ACH-000688               0              0                 0            0
## ACH-000691               0              0                 0            1
## ACH-000692               0              0                 0            0
## ACH-000693               0              0                 0            1
## ACH-000694               1              0                 0            0
## ACH-000695               1              0                 0            0
## ACH-000696               0              0                 0            1
## ACH-000697               0              0                 0            1
## ACH-000698               0              0                 0            1
## ACH-000699               0              0                 0            1
## ACH-000701               0              0                 0            0
## ACH-000703               1              0                 0            0
## ACH-000704               0              0                 1            0
## ACH-000705               0              0                 0            1
## ACH-000706               0              0                 0            1
## ACH-000708               0              0                 1            0
## ACH-000709               0              0                 0            0
## ACH-000710               0              0                 0            0
## ACH-000711               0              1                 0            0
## ACH-000712               0              0                 0            0
## ACH-000713               0              0                 0            0
## ACH-000714               0              0                 0            1
## ACH-000718               1              0                 0            0
## ACH-000719               0              0                 1            0
## ACH-000720               0              0                 0            0
## ACH-000721               1              0                 0            0
## ACH-000722               1              0                 0            0
## ACH-000724               0              0                 0            0
## ACH-000725               0              0                 0            1
## ACH-000729               0              0                 0            1
## ACH-000730               1              0                 0            0
## ACH-000731               0              0                 0            0
## ACH-000732               0              0                 0            0
## ACH-000733               0              0                 0            1
## ACH-000734               0              0                 0            1
## ACH-000735               0              0                 0            0
## ACH-000736               1              0                 0            0
## ACH-000737               0              0                 1            0
## ACH-000738               0              0                 0            1
## ACH-000739               0              0                 0            0
## ACH-000740               0              0                 0            1
## ACH-000741               0              0                 0            0
## ACH-000743               0              0                 0            1
## ACH-000744               1              0                 0            0
## ACH-000745               0              0                 0            1
## ACH-000746               1              0                 0            0
## ACH-000747               0              0                 0            1
## ACH-000748               0              0                 0            0
## ACH-000749               1              0                 0            0
## ACH-000750               1              0                 0            0
## ACH-000752               1              0                 0            0
## ACH-000753               1              0                 0            0
## ACH-000755               0              0                 0            0
## ACH-000756               0              0                 0            1
## ACH-000758               1              0                 0            0
## ACH-000759               1              0                 0            0
## ACH-000761               0              0                 1            0
## ACH-000763               0              0                 0            1
## ACH-000764               0              0                 0            1
## ACH-000765               0              0                 1            0
## ACH-000766               1              0                 0            0
## ACH-000767               1              0                 0            0
## ACH-000768               1              0                 0            0
## ACH-000769               0              0                 0            1
## ACH-000771               0              0                 0            0
## ACH-000774               0              0                 0            1
## ACH-000775               0              0                 0            1
## ACH-000776               0              0                 0            1
## ACH-000777               0              0                 0            1
## ACH-000778               1              0                 0            0
## ACH-000780               1              0                 0            0
## ACH-000781               1              0                 0            0
## ACH-000782               0              0                 0            1
## ACH-000783               1              0                 0            0
## ACH-000784               0              0                 0            1
## ACH-000785               1              0                 0            0
## ACH-000787               0              0                 0            1
## ACH-000788               1              0                 0            0
## ACH-000789               0              0                 0            1
## ACH-000790               0              0                 0            1
## ACH-000791               0              0                 0            1
## ACH-000792               0              0                 0            0
## ACH-000793               1              0                 0            0
## ACH-000794               0              0                 1            0
## ACH-000796               0              0                 0            1
## ACH-000797               0              0                 0            0
## ACH-000798               0              0                 0            0
## ACH-000799               1              0                 0            0
## ACH-000800               1              0                 0            0
## ACH-000802               0              0                 0            1
## ACH-000803               1              0                 0            0
## ACH-000804               1              0                 0            0
## ACH-000805               1              0                 0            0
## ACH-000808               0              0                 0            1
## ACH-000809               0              0                 0            1
## ACH-000810               1              0                 0            0
## ACH-000811               1              0                 0            0
## ACH-000812               1              0                 0            0
## ACH-000813               1              0                 0            0
## ACH-000815               1              0                 0            0
## ACH-000816               1              0                 0            0
## ACH-000817               0              0                 0            1
## ACH-000818               0              0                 0            1
## ACH-000819               0              0                 0            1
## ACH-000820               0              0                 0            1
## ACH-000821               0              0                 0            1
## ACH-000822               1              0                 0            0
## ACH-000823               0              0                 0            1
## ACH-000824               0              0                 0            1
## ACH-000825               0              0                 0            1
## ACH-000826               0              0                 0            1
## ACH-000828               1              0                 0            0
## ACH-000830               1              0                 0            0
## ACH-000831               1              0                 0            0
## ACH-000832               0              0                 0            1
## ACH-000833               1              0                 0            0
## ACH-000834               0              0                 1            0
## ACH-000835               1              0                 0            0
## ACH-000837               0              0                 0            1
## ACH-000838               0              0                 0            1
## ACH-000839               0              0                 0            1
## ACH-000840               0              0                 0            1
## ACH-000841               1              0                 0            0
## ACH-000842               0              0                 0            1
## ACH-000843               1              0                 0            0
## ACH-000844               0              0                 0            1
## ACH-000845               0              0                 0            1
## ACH-000846               0              0                 0            1
## ACH-000847               1              0                 0            0
## ACH-000848               0              0                 0            1
## ACH-000849               1              0                 0            0
## ACH-000850               0              1                 0            0
## ACH-000851               0              0                 0            1
## ACH-000852               0              0                 0            1
## ACH-000853               1              0                 0            0
## ACH-000855               0              0                 0            1
## ACH-000856               1              0                 0            0
## ACH-000857               0              0                 0            0
## ACH-000858               1              0                 0            0
## ACH-000859               0              0                 0            1
## ACH-000860               0              0                 0            1
## ACH-000861               0              0                 0            1
## ACH-000862               0              0                 0            1
## ACH-000863               0              0                 0            1
## ACH-000864               0              0                 0            1
## ACH-000865               0              0                 0            1
## ACH-000866               1              0                 0            0
## ACH-000867               1              0                 0            0
## ACH-000868               0              0                 0            1
## ACH-000869               1              0                 0            0
## ACH-000870               1              0                 0            0
## ACH-000871               1              0                 0            0
## ACH-000873               0              0                 0            1
## ACH-000874               0              0                 0            1
## ACH-000875               0              0                 0            1
## ACH-000876               1              0                 0            0
## ACH-000877               0              0                 0            1
## ACH-000878               0              0                 0            1
## ACH-000879               0              0                 0            1
## ACH-000880               0              0                 0            1
## ACH-000881               0              0                 0            1
## ACH-000882               1              0                 0            0
## ACH-000883               0              0                 0            1
## ACH-000884               1              0                 0            0
## ACH-000885               0              0                 0            1
## ACH-000886               1              0                 0            0
## ACH-000888               0              0                 0            1
## ACH-000889               0              0                 0            1
## ACH-000890               0              0                 0            1
## ACH-000891               0              0                 0            1
## ACH-000892               0              0                 0            1
## ACH-000893               0              0                 0            1
## ACH-000894               1              0                 0            0
## ACH-000895               0              0                 0            1
## ACH-000896               0              0                 0            1
## ACH-000897               1              0                 0            0
## ACH-000898               0              0                 0            1
## ACH-000899               1              0                 0            0
## ACH-000900               0              0                 0            1
## ACH-000901               0              0                 0            1
## ACH-000902               1              0                 0            0
## ACH-000903               1              0                 0            0
## ACH-000904               1              0                 0            0
## ACH-000906               0              0                 0            1
## ACH-000907               0              0                 0            1
## ACH-000908               0              0                 0            1
## ACH-000909               0              0                 0            1
## ACH-000910               1              0                 0            0
## ACH-000911               1              0                 0            0
## ACH-000912               0              0                 0            1
## ACH-000913               0              0                 0            1
## ACH-000915               0              0                 0            1
## ACH-000916               1              0                 0            0
## ACH-000919               0              0                 0            1
## ACH-000921               1              0                 0            0
## ACH-000924               0              0                 0            1
## ACH-000925               1              0                 0            0
## ACH-000926               0              0                 0            1
## ACH-000927               0              0                 0            1
## ACH-000928               0              0                 0            1
## ACH-000929               1              0                 0            0
## ACH-000930               0              0                 0            1
## ACH-000931               0              0                 0            1
## ACH-000932               1              0                 0            0
## ACH-000934               1              0                 0            0
## ACH-000936               1              0                 0            0
## ACH-000938               0              0                 0            1
## ACH-000939               0              0                 0            1
## ACH-000940               1              0                 0            0
## ACH-000941               0              0                 0            1
## ACH-000942               0              0                 0            1
## ACH-000943               0              0                 0            1
## ACH-000945               1              0                 0            0
## ACH-000946               0              0                 0            1
## ACH-000947               1              0                 0            0
## ACH-000948               0              0                 0            1
## ACH-000949               1              0                 0            0
## ACH-000950               1              0                 0            0
## ACH-000951               0              0                 0            1
## ACH-000952               1              0                 0            0
## ACH-000953               1              0                 0            0
## ACH-000954               0              0                 0            1
## ACH-000955               1              0                 0            0
## ACH-000956               0              0                 0            1
## ACH-000957               0              0                 0            1
## ACH-000958               0              0                 0            1
## ACH-000960               0              0                 0            1
## ACH-000961               0              0                 0            1
## ACH-000962               1              0                 0            0
## ACH-000963               1              0                 0            0
## ACH-000965               0              0                 0            1
## ACH-000966               0              0                 0            1
## ACH-000967               0              0                 0            1
## ACH-000968               1              0                 0            0
## ACH-000969               0              0                 0            1
## ACH-000971               0              0                 0            1
## ACH-000972               0              0                 0            1
## ACH-000973               0              0                 0            1
## ACH-000974               1              0                 0            0
## ACH-000976               1              0                 0            0
## ACH-000977               1              0                 0            0
## ACH-000978               0              0                 0            1
## ACH-000980               1              0                 0            0
## ACH-000981               0              0                 0            1
## ACH-000982               0              0                 0            1
## ACH-000984               0              0                 0            1
## ACH-000985               0              0                 0            1
## ACH-000987               1              0                 0            0
## ACH-000989               1              0                 0            0
## ACH-000990               0              0                 0            1
## ACH-000993               0              0                 0            1
## ACH-000994               0              0                 0            1
## ACH-000995               0              0                 0            1
## ACH-000996               0              0                 0            1
## ACH-000997               0              0                 0            1
## ACH-000998               0              0                 0            1
## ACH-001001               0              0                 0            0
## ACH-001041               0              1                 0            0
## ACH-001048               0              1                 0            0
## ACH-001061               0              0                 0            1
## ACH-001075               0              0                 1            0
## ACH-001078               0              0                 0            0
## ACH-001106               0              0                 0            0
## ACH-001113               0              0                 0            1
## ACH-001129               0              0                 0            0
## ACH-001145               1              0                 0            0
## ACH-001151               0              1                 0            0
## ACH-001163               0              1                 0            0
## ACH-001184               1              0                 0            0
## ACH-001190               1              0                 0            0
## ACH-001192               0              1                 0            0
## ACH-001194               0              1                 0            0
## ACH-001200               0              0                 1            0
## ACH-001210               0              1                 0            0
## ACH-001229               0              0                 0            0
## ACH-001239               1              0                 0            0
## ACH-001277               0              0                 1            0
## ACH-001278               0              1                 0            0
## ACH-001283               0              1                 0            0
## ACH-001306               0              0                 0            0
## ACH-001307               0              0                 0            0
## ACH-001318               0              0                 0            1
## ACH-001321               0              0                 0            0
## ACH-001328               0              0                 0            1
## ACH-001329               0              0                 0            0
## ACH-001332               0              0                 0            0
## ACH-001333               0              0                 0            1
## ACH-001334               0              0                 0            0
## ACH-001335               0              0                 0            0
## ACH-001336               1              0                 0            0
## ACH-001339               0              0                 0            0
## ACH-001340               0              1                 0            0
## ACH-001341               0              0                 0            0
## ACH-001344               1              0                 0            0
## ACH-001345               0              0                 0            1
## ACH-001346               0              0                 0            0
## ACH-001347               0              0                 0            0
## ACH-001353               0              0                 0            0
## ACH-001354               0              0                 0            0
## ACH-001356               0              0                 0            0
## ACH-001360               0              1                 0            0
## ACH-001366               1              0                 0            0
## ACH-001367               1              0                 0            0
## ACH-001368               0              1                 0            0
## ACH-001369               0              0                 0            1
## ACH-001370               0              0                 0            0
## ACH-001373               0              1                 0            0
## ACH-001374               0              0                 1            0
## ACH-001375               0              0                 0            0
## ACH-001376               0              1                 0            0
## ACH-001377               0              0                 0            1
## ACH-001378               0              0                 0            0
## ACH-001379               0              1                 0            0
## ACH-001380               0              1                 0            0
## ACH-001382               0              1                 0            0
## ACH-001384               0              1                 0            0
## ACH-001385               0              1                 0            0
## ACH-001386               1              0                 0            0
## ACH-001388               0              0                 0            0
## ACH-001389               0              0                 1            0
## ACH-001390               0              0                 0            1
## ACH-001391               0              0                 0            0
## ACH-001392               0              1                 0            0
## ACH-001394               0              1                 0            0
## ACH-001395               0              0                 1            0
## ACH-001396               0              1                 0            0
## ACH-001398               0              0                 0            1
## ACH-001399               0              0                 1            0
## ACH-001400               0              0                 0            0
## ACH-001401               0              0                 0            1
## ACH-001402               0              0                 0            1
## ACH-001403               0              1                 0            0
## ACH-001407               1              0                 0            0
## ACH-001408               0              0                 1            0
## ACH-001409               0              0                 0            0
## ACH-001410               0              1                 0            0
## ACH-001411               0              0                 0            0
## ACH-001412               0              0                 0            1
## ACH-001413               0              0                 0            1
## ACH-001414               0              0                 0            1
## ACH-001415               0              0                 0            1
## ACH-001416               0              0                 0            1
## ACH-001418               0              0                 0            0
## ACH-001419               0              0                 0            0
## ACH-001421               0              0                 0            0
## ACH-001422               0              0                 0            0
## ACH-001433               0              1                 0            0
## ACH-001441               0              1                 0            0
## ACH-001442               0              0                 1            0
## ACH-001443               0              0                 0            1
## ACH-001450               0              0                 0            0
## ACH-001451               0              0                 0            0
## ACH-001453               0              0                 0            0
## ACH-001454               0              0                 0            0
## ACH-001456               0              0                 0            0
## ACH-001458               0              0                 0            0
## ACH-001459               0              0                 0            0
## ACH-001460               0              0                 0            0
## ACH-001461               0              0                 0            0
## ACH-001484               0              0                 0            1
## ACH-001485               0              0                 0            1
## ACH-001494               0              0                 0            0
## ACH-001495               0              0                 0            0
## ACH-001496               0              0                 0            0
## ACH-001497               0              0                 0            0
## ACH-001498               1              0                 0            0
## ACH-001500               0              0                 0            0
## ACH-001509               0              0                 0            0
## ACH-001510               0              0                 0            0
## ACH-001511               0              0                 0            0
## ACH-001513               1              0                 0            0
## ACH-001515               1              0                 0            0
## ACH-001516               0              0                 0            1
## ACH-001517               0              0                 0            1
## ACH-001518               0              0                 0            1
## ACH-001519               0              0                 0            0
## ACH-001520               0              0                 0            0
## ACH-001521               0              0                 0            1
## ACH-001522               0              0                 1            0
## ACH-001523               0              0                 0            1
## ACH-001524               0              0                 0            1
## ACH-001525               1              0                 0            0
## ACH-001526               0              0                 0            0
## ACH-001528               1              0                 0            0
## ACH-001529               0              0                 0            1
## ACH-001530               1              0                 0            0
## ACH-001532               0              1                 0            0
## ACH-001536               0              0                 0            1
## ACH-001538               0              0                 0            0
## ACH-001539               0              0                 0            1
## ACH-001540               0              0                 0            0
## ACH-001541               0              0                 0            0
## ACH-001542               1              0                 0            0
## ACH-001543               0              0                 0            0
## ACH-001548               0              1                 0            0
## ACH-001549               0              0                 0            1
## ACH-001550               1              0                 0            0
## ACH-001551               1              0                 0            0
## ACH-001552               0              0                 0            1
## ACH-001554               0              0                 0            0
## ACH-001555               0              0                 0            0
## ACH-001556               0              0                 0            0
## ACH-001557               0              0                 0            0
## ACH-001558               0              0                 0            0
## ACH-001559               0              0                 0            0
## ACH-001560               0              0                 0            0
## ACH-001561               0              0                 0            0
## ACH-001562               0              0                 0            0
## ACH-001563               1              0                 0            0
## ACH-001566               1              0                 0            0
## ACH-001567               1              0                 0            0
## ACH-001568               1              0                 0            0
## ACH-001569               1              0                 0            0
## ACH-001570               1              0                 0            0
## ACH-001573               0              1                 0            0
## ACH-001574               0              0                 0            0
## ACH-001577               0              0                 0            0
## ACH-001578               0              0                 0            0
## ACH-001603               0              0                 0            0
## ACH-001605               0              0                 0            0
## ACH-001607               0              0                 1            0
## ACH-001608               0              0                 0            1
## ACH-001609               0              0                 0            0
## ACH-001610               0              0                 0            1
## ACH-001611               0              0                 0            0
## ACH-001613               0              0                 0            0
## ACH-001616               0              0                 0            0
## ACH-001617               0              0                 0            0
## ACH-001618               0              0                 0            0
## ACH-001619               0              0                 1            0
## ACH-001622               0              0                 0            0
## ACH-001623               0              0                 0            1
## ACH-001624               0              0                 0            0
## ACH-001625               1              0                 0            0
## ACH-001626               0              0                 1            0
## ACH-001627               0              0                 0            0
## ACH-001628               0              1                 0            0
## ACH-001630               0              0                 1            0
## ACH-001632               0              1                 0            0
## ACH-001634               0              0                 0            0
## ACH-001636               0              0                 0            0
## ACH-001638               0              0                 0            1
## ACH-001642               0              0                 0            0
## ACH-001645               0              0                 0            1
## ACH-001647               0              0                 1            0
## ACH-001648               0              0                 0            0
## ACH-001649               0              0                 0            0
## ACH-001650               0              0                 0            1
## ACH-001651               0              0                 0            0
## ACH-001652               0              0                 0            0
## ACH-001653               0              0                 0            1
## ACH-001654               0              0                 0            0
## ACH-001655               0              0                 0            0
## ACH-001656               0              0                 1            0
## ACH-001664               1              0                 0            0
## ACH-001668               0              0                 0            0
## ACH-001670               0              0                 0            0
## ACH-001673               0              0                 0            0
## ACH-001674               0              0                 0            1
## ACH-001677               0              0                 0            0
## ACH-001685               0              0                 0            0
## ACH-001687               0              0                 0            0
## ACH-001688               0              0                 0            0
## ACH-001690               0              0                 0            0
## ACH-001692               0              0                 0            0
## ACH-001694               0              0                 0            1
## ACH-001698               0              0                 0            0
## ACH-001699               0              0                 0            0
## ACH-001702               0              1                 0            0
## ACH-001703               0              1                 0            0
## ACH-001709               0              0                 0            1
## ACH-001711               0              0                 0            0
## ACH-001719               0              0                 0            1
## ACH-001740               0              0                 1            0
## ACH-001765               0              1                 0            0
## ACH-001786               0              0                 0            1
## ACH-001794               0              0                 0            0
## ACH-001807               0              0                 0            0
## ACH-001814               0              0                 0            0
## ACH-001818               0              1                 0            0
## ACH-001819               0              0                 1            0
## ACH-001820               0              0                 1            0
## ACH-001850               0              0                 1            0
## ACH-001861               0              0                 1            0
## ACH-001961               0              1                 0            0
## ACH-001991               0              0                 0            1
## ACH-002011               0              0                 0            0
## ACH-002015               0              0                 0            0
## ACH-002016               0              0                 0            0
## ACH-002017               0              0                 1            0
## ACH-002018               0              1                 0            0
## ACH-002019               0              0                 0            0
## ACH-002022               0              0                 0            1
## ACH-002023               0              0                 0            0
## ACH-002024               0              0                 0            1
## ACH-002025               0              0                 0            0
## ACH-002026               0              0                 0            1
## ACH-002027               0              0                 0            1
## ACH-002029               0              0                 0            1
## ACH-002038               0              0                 0            0
## ACH-002039               0              0                 1            0
## ACH-002041               0              0                 0            1
## ACH-002042               0              0                 0            0
## ACH-002044               0              0                 0            0
## ACH-002045               0              0                 0            1
## ACH-002046               0              0                 0            0
## ACH-002059               0              0                 0            1
## ACH-002062               0              0                 0            1
## ACH-002065               0              0                 1            0
## ACH-002066               0              0                 0            0
## ACH-002067               0              0                 0            0
## ACH-002069               0              0                 0            0
## ACH-002446               0              0                 1            0
## ACH-002508               1              0                 0            0
## ACH-002509               1              0                 0            0
## ACH-002510               1              0                 0            0
## ACH-002511               0              0                 0            0
##            Primary.Low Primary.Medium
## ACH-000001           0              0
## ACH-000002           1              0
## ACH-000006           1              0
## ACH-000007           0              1
## ACH-000009           0              1
## ACH-000011           0              0
## ACH-000012           1              0
## ACH-000013           0              0
## ACH-000014           0              0
## ACH-000015           0              1
## ACH-000016           0              0
## ACH-000017           0              0
## ACH-000018           1              0
## ACH-000019           0              0
## ACH-000021           0              0
## ACH-000022           0              0
## ACH-000023           0              0
## ACH-000024           0              0
## ACH-000026           0              0
## ACH-000027           1              0
## ACH-000028           0              0
## ACH-000029           0              1
## ACH-000030           0              0
## ACH-000031           1              0
## ACH-000033           0              0
## ACH-000035           0              0
## ACH-000039           0              0
## ACH-000040           1              0
## ACH-000041           1              0
## ACH-000042           1              0
## ACH-000043           0              0
## ACH-000044           0              0
## ACH-000045           1              0
## ACH-000046           0              0
## ACH-000048           1              0
## ACH-000050           0              0
## ACH-000051           1              0
## ACH-000052           1              0
## ACH-000054           0              0
## ACH-000055           0              0
## ACH-000056           0              0
## ACH-000059           1              0
## ACH-000060           1              0
## ACH-000062           0              1
## ACH-000065           1              0
## ACH-000066           0              0
## ACH-000067           1              0
## ACH-000070           1              0
## ACH-000073           1              0
## ACH-000075           1              0
## ACH-000078           0              0
## ACH-000082           1              0
## ACH-000085           1              0
## ACH-000087           1              0
## ACH-000089           0              0
## ACH-000090           0              0
## ACH-000091           0              0
## ACH-000092           0              0
## ACH-000093           1              0
## ACH-000094           0              0
## ACH-000096           1              0
## ACH-000097           0              0
## ACH-000098           1              0
## ACH-000100           0              0
## ACH-000102           1              0
## ACH-000103           0              0
## ACH-000105           1              0
## ACH-000107           1              0
## ACH-000108           0              0
## ACH-000109           0              1
## ACH-000111           1              0
## ACH-000113           1              0
## ACH-000114           0              0
## ACH-000115           0              0
## ACH-000116           0              0
## ACH-000117           0              0
## ACH-000118           0              0
## ACH-000121           0              0
## ACH-000123           1              0
## ACH-000124           1              0
## ACH-000125           0              0
## ACH-000126           0              1
## ACH-000127           0              1
## ACH-000129           0              0
## ACH-000131           1              0
## ACH-000132           0              1
## ACH-000133           1              0
## ACH-000135           1              0
## ACH-000136           1              0
## ACH-000137           1              0
## ACH-000138           0              0
## ACH-000139           1              0
## ACH-000140           0              0
## ACH-000142           1              0
## ACH-000144           0              0
## ACH-000145           1              0
## ACH-000146           0              1
## ACH-000147           0              0
## ACH-000148           1              0
## ACH-000149           0              0
## ACH-000150           1              0
## ACH-000152           1              0
## ACH-000153           0              0
## ACH-000155           1              0
## ACH-000157           0              0
## ACH-000158           0              1
## ACH-000159           0              1
## ACH-000161           0              0
## ACH-000163           1              0
## ACH-000164           1              0
## ACH-000166           0              1
## ACH-000167           0              0
## ACH-000168           0              1
## ACH-000169           0              1
## ACH-000171           1              0
## ACH-000172           0              0
## ACH-000174           1              0
## ACH-000176           1              0
## ACH-000177           0              0
## ACH-000178           0              0
## ACH-000179           0              0
## ACH-000181           0              1
## ACH-000183           0              1
## ACH-000186           0              1
## ACH-000187           1              0
## ACH-000188           1              0
## ACH-000189           0              1
## ACH-000191           0              0
## ACH-000192           0              1
## ACH-000193           1              0
## ACH-000194           1              0
## ACH-000196           0              0
## ACH-000197           0              1
## ACH-000200           0              1
## ACH-000201           1              0
## ACH-000202           0              1
## ACH-000203           0              0
## ACH-000204           0              1
## ACH-000205           0              0
## ACH-000207           0              0
## ACH-000210           0              0
## ACH-000211           0              1
## ACH-000212           0              0
## ACH-000213           0              0
## ACH-000217           0              1
## ACH-000219           0              0
## ACH-000221           0              1
## ACH-000222           0              0
## ACH-000223           0              1
## ACH-000227           0              0
## ACH-000228           1              0
## ACH-000229           1              0
## ACH-000231           0              1
## ACH-000232           0              1
## ACH-000234           1              0
## ACH-000235           0              1
## ACH-000236           0              1
## ACH-000237           0              1
## ACH-000238           0              1
## ACH-000239           0              0
## ACH-000240           1              0
## ACH-000242           1              0
## ACH-000244           1              0
## ACH-000246           0              0
## ACH-000247           0              0
## ACH-000248           0              0
## ACH-000249           1              0
## ACH-000250           0              1
## ACH-000252           0              1
## ACH-000253           0              0
## ACH-000255           0              0
## ACH-000256           0              0
## ACH-000257           0              0
## ACH-000258           0              0
## ACH-000259           0              1
## ACH-000260           0              0
## ACH-000261           0              0
## ACH-000263           0              1
## ACH-000264           0              0
## ACH-000265           0              0
## ACH-000269           0              1
## ACH-000270           0              1
## ACH-000271           0              0
## ACH-000272           1              0
## ACH-000273           1              0
## ACH-000275           0              0
## ACH-000276           0              1
## ACH-000277           0              1
## ACH-000278           0              0
## ACH-000280           0              1
## ACH-000281           0              1
## ACH-000282           0              0
## ACH-000285           0              1
## ACH-000286           0              1
## ACH-000288           1              0
## ACH-000290           0              0
## ACH-000291           0              0
## ACH-000292           0              0
## ACH-000293           1              0
## ACH-000294           0              1
## ACH-000296           0              0
## ACH-000297           0              0
## ACH-000298           0              0
## ACH-000300           0              0
## ACH-000301           0              1
## ACH-000302           0              1
## ACH-000303           0              0
## ACH-000304           0              0
## ACH-000306           1              0
## ACH-000307           0              0
## ACH-000308           0              0
## ACH-000310           0              0
## ACH-000311           0              0
## ACH-000312           0              0
## ACH-000313           0              1
## ACH-000314           0              0
## ACH-000315           0              0
## ACH-000317           0              1
## ACH-000318           0              1
## ACH-000320           0              1
## ACH-000322           0              0
## ACH-000323           1              0
## ACH-000324           0              1
## ACH-000325           0              0
## ACH-000327           1              0
## ACH-000329           1              0
## ACH-000330           0              0
## ACH-000332           0              0
## ACH-000333           1              0
## ACH-000334           0              0
## ACH-000335           0              0
## ACH-000336           1              0
## ACH-000338           0              1
## ACH-000341           0              0
## ACH-000343           0              1
## ACH-000344           0              0
## ACH-000345           0              0
## ACH-000347           0              0
## ACH-000348           0              0
## ACH-000349           0              1
## ACH-000350           0              0
## ACH-000351           0              0
## ACH-000352           0              0
## ACH-000353           0              0
## ACH-000354           0              0
## ACH-000355           0              0
## ACH-000356           0              0
## ACH-000358           0              0
## ACH-000359           1              0
## ACH-000360           0              0
## ACH-000361           0              0
## ACH-000362           0              1
## ACH-000363           0              1
## ACH-000364           0              1
## ACH-000365           0              0
## ACH-000366           0              0
## ACH-000367           0              0
## ACH-000368           0              1
## ACH-000373           0              1
## ACH-000374           1              0
## ACH-000375           0              1
## ACH-000376           0              1
## ACH-000378           0              0
## ACH-000379           0              0
## ACH-000380           0              1
## ACH-000381           0              0
## ACH-000382           0              0
## ACH-000383           0              1
## ACH-000384           0              1
## ACH-000386           0              1
## ACH-000388           0              0
## ACH-000389           0              1
## ACH-000390           0              1
## ACH-000391           0              0
## ACH-000392           0              0
## ACH-000393           0              1
## ACH-000394           0              0
## ACH-000395           0              0
## ACH-000396           0              1
## ACH-000397           0              1
## ACH-000399           0              0
## ACH-000400           0              0
## ACH-000401           0              0
## ACH-000403           0              0
## ACH-000404           0              1
## ACH-000406           0              0
## ACH-000407           0              1
## ACH-000409           0              0
## ACH-000410           0              1
## ACH-000411           1              0
## ACH-000412           0              1
## ACH-000414           0              0
## ACH-000415           1              0
## ACH-000416           0              0
## ACH-000417           0              1
## ACH-000418           1              0
## ACH-000419           0              0
## ACH-000420           0              1
## ACH-000421           0              1
## ACH-000422           0              1
## ACH-000423           0              0
## ACH-000424           0              1
## ACH-000427           0              0
## ACH-000429           0              0
## ACH-000430           0              1
## ACH-000431           0              0
## ACH-000433           0              0
## ACH-000434           0              0
## ACH-000435           0              0
## ACH-000437           0              1
## ACH-000438           0              1
## ACH-000441           0              0
## ACH-000442           0              1
## ACH-000443           0              1
## ACH-000444           0              0
## ACH-000445           0              1
## ACH-000446           0              0
## ACH-000447           0              1
## ACH-000448           0              0
## ACH-000449           0              1
## ACH-000450           0              1
## ACH-000451           0              1
## ACH-000453           0              1
## ACH-000454           0              0
## ACH-000456           0              1
## ACH-000457           0              0
## ACH-000458           0              0
## ACH-000459           0              1
## ACH-000460           0              0
## ACH-000463           0              0
## ACH-000464           0              1
## ACH-000465           0              0
## ACH-000466           0              0
## ACH-000468           0              1
## ACH-000469           0              1
## ACH-000470           0              0
## ACH-000472           0              0
## ACH-000473           0              0
## ACH-000475           0              0
## ACH-000476           0              1
## ACH-000477           0              0
## ACH-000478           0              1
## ACH-000479           0              1
## ACH-000480           0              1
## ACH-000481           0              0
## ACH-000482           0              1
## ACH-000483           0              1
## ACH-000484           1              0
## ACH-000485           0              0
## ACH-000487           0              0
## ACH-000488           0              0
## ACH-000489           0              1
## ACH-000490           0              0
## ACH-000491           0              0
## ACH-000493           0              1
## ACH-000495           0              1
## ACH-000496           0              0
## ACH-000501           0              0
## ACH-000502           0              0
## ACH-000503           0              1
## ACH-000504           0              1
## ACH-000505           0              1
## ACH-000506           0              0
## ACH-000507           0              0
## ACH-000508           0              0
## ACH-000510           0              0
## ACH-000511           0              0
## ACH-000514           0              0
## ACH-000515           0              0
## ACH-000517           0              0
## ACH-000518           0              1
## ACH-000520           0              0
## ACH-000521           0              0
## ACH-000522           0              1
## ACH-000523           0              0
## ACH-000524           0              0
## ACH-000525           0              0
## ACH-000526           1              0
## ACH-000527           0              0
## ACH-000528           0              0
## ACH-000530           0              1
## ACH-000532           0              0
## ACH-000534           0              0
## ACH-000535           1              0
## ACH-000536           0              0
## ACH-000538           0              1
## ACH-000539           1              0
## ACH-000541           0              0
## ACH-000542           0              0
## ACH-000544           0              1
## ACH-000545           0              0
## ACH-000546           0              0
## ACH-000547           0              1
## ACH-000548           0              0
## ACH-000550           0              0
## ACH-000551           0              0
## ACH-000552           0              0
## ACH-000553           0              0
## ACH-000554           0              0
## ACH-000555           1              0
## ACH-000557           1              0
## ACH-000558           0              1
## ACH-000559           0              0
## ACH-000561           0              0
## ACH-000562           0              0
## ACH-000563           0              0
## ACH-000564           0              0
## ACH-000565           0              0
## ACH-000566           0              1
## ACH-000568           0              1
## ACH-000569           1              0
## ACH-000570           0              0
## ACH-000571           0              1
## ACH-000572           0              1
## ACH-000573           0              0
## ACH-000574           0              0
## ACH-000576           0              0
## ACH-000577           0              0
## ACH-000578           0              1
## ACH-000579           0              0
## ACH-000580           0              1
## ACH-000581           0              0
## ACH-000582           0              0
## ACH-000584           0              0
## ACH-000585           0              0
## ACH-000586           0              0
## ACH-000587           0              1
## ACH-000588           0              0
## ACH-000589           0              0
## ACH-000590           0              0
## ACH-000593           0              1
## ACH-000594           0              0
## ACH-000595           0              0
## ACH-000596           0              0
## ACH-000598           0              0
## ACH-000599           0              1
## ACH-000600           1              0
## ACH-000601           0              1
## ACH-000603           0              0
## ACH-000606           1              0
## ACH-000607           0              0
## ACH-000608           0              1
## ACH-000609           0              1
## ACH-000610           0              0
## ACH-000611           0              0
## ACH-000613           1              0
## ACH-000614           0              0
## ACH-000616           0              0
## ACH-000617           0              0
## ACH-000619           0              1
## ACH-000620           0              0
## ACH-000621           0              0
## ACH-000622           0              0
## ACH-000623           0              1
## ACH-000624           0              1
## ACH-000625           0              1
## ACH-000627           0              0
## ACH-000628           0              0
## ACH-000631           0              0
## ACH-000632           0              0
## ACH-000633           0              0
## ACH-000635           0              0
## ACH-000637           0              0
## ACH-000638           0              0
## ACH-000639           0              0
## ACH-000640           0              0
## ACH-000643           0              0
## ACH-000644           0              1
## ACH-000645           1              0
## ACH-000646           0              0
## ACH-000647           0              0
## ACH-000648           0              0
## ACH-000649           0              0
## ACH-000650           0              0
## ACH-000651           0              0
## ACH-000652           0              0
## ACH-000653           0              1
## ACH-000655           0              1
## ACH-000656           0              0
## ACH-000657           0              0
## ACH-000658           0              0
## ACH-000659           0              0
## ACH-000660           0              1
## ACH-000662           0              0
## ACH-000663           0              0
## ACH-000665           0              0
## ACH-000666           0              0
## ACH-000667           0              0
## ACH-000668           0              1
## ACH-000669           0              0
## ACH-000670           0              0
## ACH-000672           0              0
## ACH-000674           0              0
## ACH-000675           0              0
## ACH-000677           0              1
## ACH-000678           0              0
## ACH-000679           0              0
## ACH-000680           0              0
## ACH-000681           0              0
## ACH-000683           0              0
## ACH-000684           0              1
## ACH-000685           0              0
## ACH-000686           0              1
## ACH-000688           1              0
## ACH-000691           0              0
## ACH-000692           0              1
## ACH-000693           0              0
## ACH-000694           0              0
## ACH-000695           0              0
## ACH-000696           0              0
## ACH-000697           0              0
## ACH-000698           0              0
## ACH-000699           0              0
## ACH-000701           0              1
## ACH-000703           0              0
## ACH-000704           0              0
## ACH-000705           0              0
## ACH-000706           0              0
## ACH-000708           0              0
## ACH-000709           0              1
## ACH-000710           1              0
## ACH-000711           0              0
## ACH-000712           0              1
## ACH-000713           0              1
## ACH-000714           0              0
## ACH-000718           0              0
## ACH-000719           0              0
## ACH-000720           0              1
## ACH-000721           0              0
## ACH-000722           0              0
## ACH-000724           0              1
## ACH-000725           0              0
## ACH-000729           0              0
## ACH-000730           0              0
## ACH-000731           1              0
## ACH-000732           1              0
## ACH-000733           0              0
## ACH-000734           0              0
## ACH-000735           0              1
## ACH-000736           0              0
## ACH-000737           0              0
## ACH-000738           0              0
## ACH-000739           0              1
## ACH-000740           0              0
## ACH-000741           0              1
## ACH-000743           0              0
## ACH-000744           0              0
## ACH-000745           0              0
## ACH-000746           0              0
## ACH-000747           0              0
## ACH-000748           0              1
## ACH-000749           0              0
## ACH-000750           0              0
## ACH-000752           0              0
## ACH-000753           0              0
## ACH-000755           0              1
## ACH-000756           0              0
## ACH-000758           0              0
## ACH-000759           0              0
## ACH-000761           0              0
## ACH-000763           0              0
## ACH-000764           0              0
## ACH-000765           0              0
## ACH-000766           0              0
## ACH-000767           0              0
## ACH-000768           0              0
## ACH-000769           0              0
## ACH-000771           0              1
## ACH-000774           0              0
## ACH-000775           0              0
## ACH-000776           0              0
## ACH-000777           0              0
## ACH-000778           0              0
## ACH-000780           0              0
## ACH-000781           0              0
## ACH-000782           0              0
## ACH-000783           0              0
## ACH-000784           0              0
## ACH-000785           0              0
## ACH-000787           0              0
## ACH-000788           0              0
## ACH-000789           0              0
## ACH-000790           0              0
## ACH-000791           0              0
## ACH-000792           0              1
## ACH-000793           0              0
## ACH-000794           0              0
## ACH-000796           0              0
## ACH-000797           0              1
## ACH-000798           0              1
## ACH-000799           0              0
## ACH-000800           0              0
## ACH-000802           0              0
## ACH-000803           0              0
## ACH-000804           0              0
## ACH-000805           0              0
## ACH-000808           0              0
## ACH-000809           0              0
## ACH-000810           0              0
## ACH-000811           0              0
## ACH-000812           0              0
## ACH-000813           0              0
## ACH-000815           0              0
## ACH-000816           0              0
## ACH-000817           0              0
## ACH-000818           0              0
## ACH-000819           0              0
## ACH-000820           0              0
## ACH-000821           0              0
## ACH-000822           0              0
## ACH-000823           0              0
## ACH-000824           0              0
## ACH-000825           0              0
## ACH-000826           0              0
## ACH-000828           0              0
## ACH-000830           0              0
## ACH-000831           0              0
## ACH-000832           0              0
## ACH-000833           0              0
## ACH-000834           0              0
## ACH-000835           0              0
## ACH-000837           0              0
## ACH-000838           0              0
## ACH-000839           0              0
## ACH-000840           0              0
## ACH-000841           0              0
## ACH-000842           0              0
## ACH-000843           0              0
## ACH-000844           0              0
## ACH-000845           0              0
## ACH-000846           0              0
## ACH-000847           0              0
## ACH-000848           0              0
## ACH-000849           0              0
## ACH-000850           0              0
## ACH-000851           0              0
## ACH-000852           0              0
## ACH-000853           0              0
## ACH-000855           0              0
## ACH-000856           0              0
## ACH-000857           0              1
## ACH-000858           0              0
## ACH-000859           0              0
## ACH-000860           0              0
## ACH-000861           0              0
## ACH-000862           0              0
## ACH-000863           0              0
## ACH-000864           0              0
## ACH-000865           0              0
## ACH-000866           0              0
## ACH-000867           0              0
## ACH-000868           0              0
## ACH-000869           0              0
## ACH-000870           0              0
## ACH-000871           0              0
## ACH-000873           0              0
## ACH-000874           0              0
## ACH-000875           0              0
## ACH-000876           0              0
## ACH-000877           0              0
## ACH-000878           0              0
## ACH-000879           0              0
## ACH-000880           0              0
## ACH-000881           0              0
## ACH-000882           0              0
## ACH-000883           0              0
## ACH-000884           0              0
## ACH-000885           0              0
## ACH-000886           0              0
## ACH-000888           0              0
## ACH-000889           0              0
## ACH-000890           0              0
## ACH-000891           0              0
## ACH-000892           0              0
## ACH-000893           0              0
## ACH-000894           0              0
## ACH-000895           0              0
## ACH-000896           0              0
## ACH-000897           0              0
## ACH-000898           0              0
## ACH-000899           0              0
## ACH-000900           0              0
## ACH-000901           0              0
## ACH-000902           0              0
## ACH-000903           0              0
## ACH-000904           0              0
## ACH-000906           0              0
## ACH-000907           0              0
## ACH-000908           0              0
## ACH-000909           0              0
## ACH-000910           0              0
## ACH-000911           0              0
## ACH-000912           0              0
## ACH-000913           0              0
## ACH-000915           0              0
## ACH-000916           0              0
## ACH-000919           0              0
## ACH-000921           0              0
## ACH-000924           0              0
## ACH-000925           0              0
## ACH-000926           0              0
## ACH-000927           0              0
## ACH-000928           0              0
## ACH-000929           0              0
## ACH-000930           0              0
## ACH-000931           0              0
## ACH-000932           0              0
## ACH-000934           0              0
## ACH-000936           0              0
## ACH-000938           0              0
## ACH-000939           0              0
## ACH-000940           0              0
## ACH-000941           0              0
## ACH-000942           0              0
## ACH-000943           0              0
## ACH-000945           0              0
## ACH-000946           0              0
## ACH-000947           0              0
## ACH-000948           0              0
## ACH-000949           0              0
## ACH-000950           0              0
## ACH-000951           0              0
## ACH-000952           0              0
## ACH-000953           0              0
## ACH-000954           0              0
## ACH-000955           0              0
## ACH-000956           0              0
## ACH-000957           0              0
## ACH-000958           0              0
## ACH-000960           0              0
## ACH-000961           0              0
## ACH-000962           0              0
## ACH-000963           0              0
## ACH-000965           0              0
## ACH-000966           0              0
## ACH-000967           0              0
## ACH-000968           0              0
## ACH-000969           0              0
## ACH-000971           0              0
## ACH-000972           0              0
## ACH-000973           0              0
## ACH-000974           0              0
## ACH-000976           0              0
## ACH-000977           0              0
## ACH-000978           0              0
## ACH-000980           0              0
## ACH-000981           0              0
## ACH-000982           0              0
## ACH-000984           0              0
## ACH-000985           0              0
## ACH-000987           0              0
## ACH-000989           0              0
## ACH-000990           0              0
## ACH-000993           0              0
## ACH-000994           0              0
## ACH-000995           0              0
## ACH-000996           0              0
## ACH-000997           0              0
## ACH-000998           0              0
## ACH-001001           0              1
## ACH-001041           0              0
## ACH-001048           0              0
## ACH-001061           0              0
## ACH-001075           0              0
## ACH-001078           0              1
## ACH-001106           0              1
## ACH-001113           0              0
## ACH-001129           1              0
## ACH-001145           0              0
## ACH-001151           0              0
## ACH-001163           0              0
## ACH-001184           0              0
## ACH-001190           0              0
## ACH-001192           0              0
## ACH-001194           0              0
## ACH-001200           0              0
## ACH-001210           0              0
## ACH-001229           1              0
## ACH-001239           0              0
## ACH-001277           0              0
## ACH-001278           0              0
## ACH-001283           0              0
## ACH-001306           0              1
## ACH-001307           0              1
## ACH-001318           0              0
## ACH-001321           0              1
## ACH-001328           0              0
## ACH-001329           0              1
## ACH-001332           1              0
## ACH-001333           0              0
## ACH-001334           0              1
## ACH-001335           0              1
## ACH-001336           0              0
## ACH-001339           0              1
## ACH-001340           0              0
## ACH-001341           0              1
## ACH-001344           0              0
## ACH-001345           0              0
## ACH-001346           1              0
## ACH-001347           1              0
## ACH-001353           1              0
## ACH-001354           1              0
## ACH-001356           1              0
## ACH-001360           0              0
## ACH-001366           0              0
## ACH-001367           0              0
## ACH-001368           0              0
## ACH-001369           0              0
## ACH-001370           1              0
## ACH-001373           0              0
## ACH-001374           0              0
## ACH-001375           1              0
## ACH-001376           0              0
## ACH-001377           0              0
## ACH-001378           1              0
## ACH-001379           0              0
## ACH-001380           0              0
## ACH-001382           0              0
## ACH-001384           0              0
## ACH-001385           0              0
## ACH-001386           0              0
## ACH-001388           1              0
## ACH-001389           0              0
## ACH-001390           0              0
## ACH-001391           1              0
## ACH-001392           0              0
## ACH-001394           0              0
## ACH-001395           0              0
## ACH-001396           0              0
## ACH-001398           0              0
## ACH-001399           0              0
## ACH-001400           0              1
## ACH-001401           0              0
## ACH-001402           0              0
## ACH-001403           0              0
## ACH-001407           0              0
## ACH-001408           0              0
## ACH-001409           0              1
## ACH-001410           0              0
## ACH-001411           0              1
## ACH-001412           0              0
## ACH-001413           0              0
## ACH-001414           0              0
## ACH-001415           0              0
## ACH-001416           0              0
## ACH-001418           1              0
## ACH-001419           1              0
## ACH-001421           1              0
## ACH-001422           1              0
## ACH-001433           0              0
## ACH-001441           0              0
## ACH-001442           0              0
## ACH-001443           0              0
## ACH-001450           1              0
## ACH-001451           1              0
## ACH-001453           1              0
## ACH-001454           1              0
## ACH-001456           1              0
## ACH-001458           0              1
## ACH-001459           1              0
## ACH-001460           1              0
## ACH-001461           1              0
## ACH-001484           0              0
## ACH-001485           0              0
## ACH-001494           0              1
## ACH-001495           1              0
## ACH-001496           0              1
## ACH-001497           0              1
## ACH-001498           0              0
## ACH-001500           0              1
## ACH-001509           1              0
## ACH-001510           0              1
## ACH-001511           1              0
## ACH-001513           0              0
## ACH-001515           0              0
## ACH-001516           0              0
## ACH-001517           0              0
## ACH-001518           0              0
## ACH-001519           0              1
## ACH-001520           1              0
## ACH-001521           0              0
## ACH-001522           0              0
## ACH-001523           0              0
## ACH-001524           0              0
## ACH-001525           0              0
## ACH-001526           0              1
## ACH-001528           0              0
## ACH-001529           0              0
## ACH-001530           0              0
## ACH-001532           0              0
## ACH-001536           0              0
## ACH-001538           0              1
## ACH-001539           0              0
## ACH-001540           0              1
## ACH-001541           0              1
## ACH-001542           0              0
## ACH-001543           0              1
## ACH-001548           0              0
## ACH-001549           0              0
## ACH-001550           0              0
## ACH-001551           0              0
## ACH-001552           0              0
## ACH-001554           1              0
## ACH-001555           1              0
## ACH-001556           1              0
## ACH-001557           1              0
## ACH-001558           1              0
## ACH-001559           1              0
## ACH-001560           1              0
## ACH-001561           1              0
## ACH-001562           1              0
## ACH-001563           0              0
## ACH-001566           0              0
## ACH-001567           0              0
## ACH-001568           0              0
## ACH-001569           0              0
## ACH-001570           0              0
## ACH-001573           0              0
## ACH-001574           1              0
## ACH-001577           1              0
## ACH-001578           0              1
## ACH-001603           0              1
## ACH-001605           0              1
## ACH-001607           0              0
## ACH-001608           0              0
## ACH-001609           0              1
## ACH-001610           0              0
## ACH-001611           0              1
## ACH-001613           1              0
## ACH-001616           1              0
## ACH-001617           1              0
## ACH-001618           1              0
## ACH-001619           0              0
## ACH-001622           0              1
## ACH-001623           0              0
## ACH-001624           0              1
## ACH-001625           0              0
## ACH-001626           0              0
## ACH-001627           1              0
## ACH-001628           0              0
## ACH-001630           0              0
## ACH-001632           0              0
## ACH-001634           1              0
## ACH-001636           1              0
## ACH-001638           0              0
## ACH-001642           0              1
## ACH-001645           0              0
## ACH-001647           0              0
## ACH-001648           1              0
## ACH-001649           1              0
## ACH-001650           0              0
## ACH-001651           1              0
## ACH-001652           0              1
## ACH-001653           0              0
## ACH-001654           1              0
## ACH-001655           0              1
## ACH-001656           0              0
## ACH-001664           0              0
## ACH-001668           1              0
## ACH-001670           0              1
## ACH-001673           0              1
## ACH-001674           0              0
## ACH-001677           1              0
## ACH-001685           0              1
## ACH-001687           0              1
## ACH-001688           0              1
## ACH-001690           1              0
## ACH-001692           1              0
## ACH-001694           0              0
## ACH-001698           1              0
## ACH-001699           0              1
## ACH-001702           0              0
## ACH-001703           0              0
## ACH-001709           0              0
## ACH-001711           1              0
## ACH-001719           0              0
## ACH-001740           0              0
## ACH-001765           0              0
## ACH-001786           0              0
## ACH-001794           1              0
## ACH-001807           1              0
## ACH-001814           1              0
## ACH-001818           0              0
## ACH-001819           0              0
## ACH-001820           0              0
## ACH-001850           0              0
## ACH-001861           0              0
## ACH-001961           0              0
## ACH-001991           0              0
## ACH-002011           1              0
## ACH-002015           1              0
## ACH-002016           1              0
## ACH-002017           0              0
## ACH-002018           0              0
## ACH-002019           0              1
## ACH-002022           0              0
## ACH-002023           0              1
## ACH-002024           0              0
## ACH-002025           0              1
## ACH-002026           0              0
## ACH-002027           0              0
## ACH-002029           0              0
## ACH-002038           0              1
## ACH-002039           0              0
## ACH-002041           0              0
## ACH-002042           0              1
## ACH-002044           0              1
## ACH-002045           0              0
## ACH-002046           0              1
## ACH-002059           0              0
## ACH-002062           0              0
## ACH-002065           0              0
## ACH-002066           0              1
## ACH-002067           0              1
## ACH-002069           0              1
## ACH-002446           0              0
## ACH-002508           0              0
## ACH-002509           0              0
## ACH-002510           0              0
## ACH-002511           1              0
## attr(,"assign")
## [1] 1 1 1 1 1 1
## attr(,"contrasts")
## attr(,"contrasts")$Group
## [1] "contr.treatment"

##        MHvsPH MLvsPL MHvsML PHvsPL MHvsPL PHvsML
## Down      395    288   1247   3343   3603   1663
## NotSig  24452  25136  22773  18323  16752  22572
## Up        899    322   1726   4080   5391   1511
##                      logFC     AveExpr          t      P.Value    adj.P.Val
## ENSG00000246430 -2.4408491 -5.87807662 -10.159632 3.659674e-23 9.422196e-19
## ENSG00000183305  4.2771331 -2.13010423   9.102870 4.531851e-19 5.833851e-15
## ENSG00000132274 -3.4277661  1.64846236  -9.043341 7.513842e-19 6.448380e-15
## ENSG00000268606  4.4404464 -1.42482359   8.960674 1.509436e-18 9.715482e-15
## ENSG00000277363  2.2837677  1.54239804   8.927157 1.999810e-18 1.029742e-14
## ENSG00000197172  4.4024882  0.05658333   8.689111 1.437818e-17 6.169677e-14
## ENSG00000169857 -0.7769217  3.53459179  -8.455885 9.511237e-17 3.060954e-13
## ENSG00000166710 -1.4130402  9.57623409  -8.468934 8.566925e-17 3.060954e-13
## ENSG00000224271  2.6623087 -3.39097971   8.413178 1.337986e-16 3.827533e-13
## ENSG00000279753 -1.7523331  0.80568349  -8.393601 1.563804e-16 4.026170e-13
##                        B
## ENSG00000246430 41.19648
## ENSG00000183305 32.21412
## ENSG00000132274 32.00096
## ENSG00000268606 31.10127
## ENSG00000277363 30.98745
## ENSG00000197172 29.01167
## ENSG00000169857 27.34579
## ENSG00000166710 26.86482
## ENSG00000224271 26.74426
## ENSG00000279753 26.73454

##        MHvsPH MLvsPL MHvsML PHvsPL MHvsPL PHvsML
## Down        4     13    100    889    950    231
## NotSig  25695  25714  25477  23973  23131  25422
## Up         47     19    169    884   1665     93
##                     logFC     AveExpr         t      P.Value    adj.P.Val
## ENSG00000246430 -2.440849 -5.87807662 -9.064795 3.132069e-19 8.063824e-15
## ENSG00000183305  4.277133 -2.13010423  8.543063 2.358977e-17 3.036711e-13
## ENSG00000268606  4.440446 -1.42482359  8.429879 5.855893e-17 5.025527e-13
## ENSG00000132274 -3.427766  1.64846236 -8.349387 1.110790e-16 7.149602e-13
## ENSG00000197172  4.402488  0.05658333  8.169965 4.544392e-16 2.339998e-12
## ENSG00000277363  2.283768  1.54239804  7.898966 3.630208e-15 1.557722e-11
## ENSG00000224271  2.662309 -3.39097971  7.581961 3.824443e-14 1.406630e-10
## ENSG00000221867  4.203742  0.53575432  7.551791 4.766560e-14 1.533998e-10
## ENSG00000213401  3.855132 -0.96422466  7.517475 6.113278e-14 1.748805e-10
## ENSG00000279753 -1.752333  0.80568349 -7.133677 9.265418e-13 2.385475e-09
##                     logFC      AveExpr         t      P.Value    adj.P.Val
## ENSG00000246430 -2.079330 -5.878076622 -8.019834 1.447411e-15 3.726503e-11
## ENSG00000132274 -2.738173  1.648462364 -7.483681 7.803565e-14 1.004553e-09
## ENSG00000231240  2.609696 -4.038266083  7.163147 7.552882e-13 4.465378e-09
## ENSG00000169554 -3.097098  1.664564089 -7.143501 8.656336e-13 4.465378e-09
## ENSG00000154175 -2.438812 -0.003401133 -7.143234 8.671984e-13 4.465378e-09
## ENSG00000180178  3.159914 -1.458796036  6.935929 3.582940e-12 1.537440e-08
## ENSG00000126947 -3.045818  0.075321107 -6.908264 4.317650e-12 1.588032e-08
## ENSG00000251026  2.411530 -3.743433473  6.790641 9.473904e-12 3.048939e-08
## ENSG00000221852 -2.110220 -5.236553221 -6.621908 2.865415e-11 8.196998e-08
## ENSG00000224271  2.176765 -3.390979711  6.459792 8.109674e-11 2.087917e-07

## Warning in makeAnno(x, anno): No gene annotation provided.

##      query significant      p_value term_size query_size intersection_size
## 1  query_1        TRUE 5.709244e-49      7322       1487               794
## 2  query_1        TRUE 4.044119e-40      6553       1487               709
## 3  query_1        TRUE 4.384922e-39      5997       1487               662
## 4  query_1        TRUE 1.324471e-38      4053       1487               499
## 5  query_1        TRUE 4.869980e-38      4727       1487               555
## 6  query_1        TRUE 1.525063e-37      1530       1487               256
## 7  query_1        TRUE 3.364042e-37      6540       1487               699
## 8  query_1        TRUE 3.490296e-37      6515       1487               697
## 9  query_1        TRUE 1.395714e-33      8999       1487               871
## 10 query_1        TRUE 1.069665e-31      6002       1487               639
##    precision     recall    term_id source                          term_name
## 1  0.5339610 0.10844032 GO:0032501  GO:BP   multicellular organismal process
## 2  0.4767989 0.10819472 GO:0032502  GO:BP              developmental process
## 3  0.4451917 0.11038853 GO:0048856  GO:BP   anatomical structure development
## 4  0.3355750 0.12311868 GO:0048731  GO:BP                 system development
## 5  0.3732347 0.11741062 GO:0007275  GO:BP multicellular organism development
## 6  0.1721587 0.16732026 GO:0007155  GO:BP                      cell adhesion
## 7  0.4700740 0.10688073 GO:0007154  GO:BP                 cell communication
## 8  0.4687290 0.10698388 GO:0023052  GO:BP                          signaling
## 9  0.5857431 0.09678853 GO:0050896  GO:BP               response to stimulus
## 10 0.4297243 0.10646451 GO:0007165  GO:BP                signal transduction
##    effective_domain_size source_order      parents
## 1                  21026         7557   GO:0008150
## 2                  21026         7558   GO:0008150
## 3                  21026        12931   GO:0032502
## 4                  21026        12821 GO:00072....
## 5                  21026         2788 GO:00325....
## 6                  21026         2706   GO:0009987
## 7                  21026         2705   GO:0009987
## 8                  21026         6607   GO:0050789
## 9                  21026        13167   GO:0008150
## 10                 21026         2716 GO:00071....
##      query significant      p_value term_size query_size intersection_size
## 1  query_1        TRUE 3.254949e-34      1534       1063               201
## 2  query_1        TRUE 1.624975e-32      7322       1063               564
## 3  query_1        TRUE 3.787749e-32      2713       1063               284
## 4  query_1        TRUE 2.458910e-31      1530       1063               195
## 5  query_1        TRUE 4.197300e-31      5997       1063               486
## 6  query_1        TRUE 1.632578e-30      4053       1063               368
## 7  query_1        TRUE 2.893900e-30      6553       1063               515
## 8  query_1        TRUE 4.047618e-30       960       1063               145
## 9  query_1        TRUE 1.036108e-29      1793       1063               212
## 10 query_1        TRUE 6.441011e-29      1255       1063               168
##    precision     recall    term_id source                          term_name
## 1  0.1890875 0.13102999 GO:0016477  GO:BP                     cell migration
## 2  0.5305738 0.07702813 GO:0032501  GO:BP   multicellular organismal process
## 3  0.2671684 0.10468116 GO:0009653  GO:BP anatomical structure morphogenesis
## 4  0.1834431 0.12745098 GO:0007155  GO:BP                      cell adhesion
## 5  0.4571966 0.08104052 GO:0048856  GO:BP   anatomical structure development
## 6  0.3461900 0.09079694 GO:0048731  GO:BP                 system development
## 7  0.4844779 0.07858996 GO:0032502  GO:BP              developmental process
## 8  0.1364064 0.15104167 GO:0030334  GO:BP       regulation of cell migration
## 9  0.1994356 0.11823759 GO:0048870  GO:BP                      cell motility
## 10 0.1580433 0.13386454 GO:0040011  GO:BP                         locomotion
##    effective_domain_size source_order      parents
## 1                  21026         5204   GO:0048870
## 2                  21026         7557   GO:0008150
## 3                  21026         3557 GO:00325....
## 4                  21026         2706   GO:0009987
## 5                  21026        12931   GO:0032502
## 6                  21026        12821 GO:00072....
## 7                  21026         7558   GO:0008150
## 8                  21026         6743 GO:00164....
## 9                  21026        12944   GO:0009987
## 10                 21026         9808   GO:0008150

Multiple contrasts across combined groups were evaluated. After filtering 20,307 genes remained. MHvsPL had many differential genes; TREAT reduced counts but still left substantial numbers. GO analyses reflect underexpression of immune response terms for MHvsPL and changes related to ECM and cell migration for PHvsPL.

Back to analysis

6 Multivariate analysis

6.2 Unsupervised analysis

6.2.2 Principal Component Analysis (PCA)

##        eigenvalue variance.percent cumulative.variance.percent
## Dim.1   223.43053        25.228846                    25.22885
## Dim.2    83.20050         9.394655                    34.62350
## Dim.3    56.93482         6.428843                    41.05234
## Dim.4    39.36907         4.445391                    45.49774
## Dim.5    34.19801         3.861497                    49.35923
## Dim.6    27.98429         3.159870                    52.51910
## Dim.7    20.72826         2.340549                    54.85965
## Dim.8    19.14781         2.162091                    57.02174
## Dim.9    17.31825         1.955505                    58.97725
## Dim.10   16.51059         1.864307                    60.84155
## [1] 47

PCA shows first three components explain ~40% variance; some trend of Primary.High grouping on negative PC1, but not a clear separation.

6.2.3 k-means clustering

De forma a efetuar um k-means clustering sobre o dataset afim de encontrar os clusters teóricos, foi construído um silhouette plot para verificar o número ótimo de clusters a utilizar, tendo-se optado por \(2\) clusters.
De seguida, foi efetuado o clustering em si tendo resultado em 2 grupos que se separam uniformemente ao longo do primeiro componente.
A comparação destes clusters com aqueles obtidos pela sobreposição da informação dos grupos reforça a conclusão anterior da má separação das linhagens por esta característica ao longo do mapa fatorial.

6.2.4 Análise supervisionada (Machine Learning)

Mediante os resultados antes obtidos, propusemo-nos a construir um modelo de machine learning para efetuar a previsão da ação da simvastatina sobre as linhagens celulares estando isto representado na classificação das linhagens como tendo uma baixa ação (“Low”) ou uma alta ação (“High”) da simvastatina. Foram usados \(100\) genes preditores provenientes da expressão diferencial, juntamente com \(559\) linhagens cancerígenas.

Para tal foram testadas 5 frameworks: “Neural Networks”, “Random Forest”, “Decision Trees”, “K Nearest Neighbors” e “Naïve Bayes”.

Em todos os modelos foi utilizada uma estimação do erro corresponde a validação cruzada com 10 folds repetida 5 vezes, aquando da sua construção. De forma a tornar estes resultados replicáveis, foi invocada uma seed de valor “16718”.

Neural Networks

## Neural Network 
## 
## 403 samples
## 100 predictors
##   2 classes: '1', '2' 
## 
## No pre-processing
## Resampling: Cross-Validated (10 fold, repeated 5 times) 
## Summary of sample sizes: 363, 363, 362, 363, 363, 362, ... 
## Resampling results across tuning parameters:
## 
##   size  decay  Accuracy   Kappa     
##   1     0e+00  0.6622483  0.15694938
##   1     1e-04  0.6356751  0.09596943
##   1     1e-01  0.7445503  0.46214191
##   3     0e+00  0.7199278  0.37808896
##   3     1e-04  0.7392211  0.41720434
##   3     1e-01  0.7407724  0.44808694
##   5     0e+00  0.7403327  0.42262363
##   5     1e-04  0.7412486  0.44878799
##   5     1e-01  0.7432389  0.45620617
## 
## Accuracy was used to select the optimal model using the largest value.
## The final values used for the model were size = 1 and decay = 0.1.

Na construção do modelo por “Neural Networks” foi dado o argumento “tuneLenght = 10”, correspondendo isto ao número combinações aleatórias de hiperparâmetros possíveis a utilizar pelo algoritmo na sua construção.
Obtivemos que os parâmetros selecionados correspondem a um “size” 1 (número de unidades na camada intermédia) e a um “decay” (regularização para evitar sobreajustamento) de 0.1, possuindo o modelo uma precisão de aproximadamente \(0.62\).

Voltar à análise

Random Forests

## Random Forest 
## 
## 403 samples
## 100 predictors
##   2 classes: '1', '2' 
## 
## No pre-processing
## Resampling: Cross-Validated (10 fold, repeated 5 times) 
## Summary of sample sizes: 363, 363, 362, 363, 363, 362, ... 
## Resampling results across tuning parameters:
## 
##   mtry  Accuracy   Kappa    
##     2   0.7809500  0.5227332
##    51   0.7845744  0.5370620
##   100   0.7810231  0.5284431
## 
## Accuracy was used to select the optimal model using the largest value.
## The final value used for the model was mtry = 51.

Na construção do modelo por “Random Forest” foi dado o argumento “tuneLenght = 10”, correspondendo isto ao número combinações aleatórias de hiperparâmetros possíveis a utilizar pelo algoritmo na sua construção.
Obtivemos que os parâmetros selecionados correspondem a um “mtry” de 2 (número de variáveis randomizadamente amostradas como candidatas a cada ramificação), possuindo o modelo uma precisão de aproximadamente \(0.63\).

Voltar à análise

Decision Trees

## CART 
## 
## 403 samples
## 100 predictors
##   2 classes: '1', '2' 
## 
## No pre-processing
## Resampling: Cross-Validated (10 fold, repeated 5 times) 
## Summary of sample sizes: 363, 363, 362, 363, 363, 362, ... 
## Resampling results:
## 
##   Accuracy   Kappa    
##   0.7055594  0.3844856
## 
## Tuning parameter 'cp' was held constant at a value of 0.2

Na construção do modelo por “Decision Trees” foi dado o argumento “expand.grid = (.cp=0.2)”, correspondendo isto ao número combinações aleatórias de hiperparâmetros possíveis a utilizar pelo algoritmo na sua construção.
Obtivemos que os parâmetros selecionados correspondem a um “cp” a um valor constante de 0.2 (complexidade do parâmetro e dos valores de erro associados), possuindo o modelo uma precisão de aproximadamente \(0.58\).

Voltar à análise

k Nearest Neighbors

## k-Nearest Neighbors 
## 
## 403 samples
## 100 predictors
##   2 classes: '1', '2' 
## 
## No pre-processing
## Resampling: Cross-Validated (10 fold, repeated 5 times) 
## Summary of sample sizes: 363, 363, 362, 363, 363, 362, ... 
## Resampling results across tuning parameters:
## 
##   k   Accuracy   Kappa    
##    1  0.7123027  0.4017940
##    2  0.7148906  0.4105248
##    3  0.7381620  0.4513294
##    4  0.7347602  0.4452555
##    5  0.7401742  0.4519324
##    6  0.7529278  0.4817922
##    7  0.7565553  0.4916879
##    8  0.7615450  0.5005876
##    9  0.7576041  0.4946542
##   10  0.7546901  0.4870555
## 
## Accuracy was used to select the optimal model using the largest value.
## The final value used for the model was k = 8.

Na construção do modelo por “k Nearest Neighbours” foi dado o argumento “tuneLenght = expand.grid = (1:10)”, ou seja o número de vizinhos a ser implementados pelo algoritmo.
Obtivemos que os parâmetros selecionados correspondem a um “k” de 10 (número de vizinhos), possuindo o modelo uma precisão de aproximadamente \(0.62\).

Voltar à análise

Naïve Bayes

## Naive Bayes 
## 
## 403 samples
## 100 predictors
##   2 classes: '1', '2' 
## 
## No pre-processing
## Resampling: Cross-Validated (10 fold, repeated 5 times) 
## Summary of sample sizes: 363, 363, 362, 363, 363, 362, ... 
## Resampling results across tuning parameters:
## 
##   usekernel  Accuracy   Kappa    
##   FALSE      0.7663962  0.5205076
##    TRUE      0.6727630  0.3830728
## 
## Tuning parameter 'fL' was held constant at a value of 0
## Tuning
##  parameter 'adjust' was held constant at a value of 1
## Accuracy was used to select the optimal model using the largest value.
## The final values used for the model were fL = 0, usekernel = FALSE and adjust
##  = 1.

Na construção do modelo por “Naïve Bayes” foi dado o argumento “tuneLenght = 10”, correspondendo isto ao número combinações aleatórias de hiperparâmetros possíveis a utilizar pelo algoritmo na sua construção.
Obtivemos que os parâmetros selecionados correspondem a um “fL” de 0 (incorporação da suavização de Laplace), a ausência do uso de um “kernel” (uso de uma kernel density estimate) e um “adjust = 1” (ajuste da largura de banda da da kernel density), possuindo o modelo uma precisão de aproximadamente \(0.63\).

Voltar à análise

6.2.5 Resultados machine learning

Após observação da precisão dos 5 modelos para a classificação das linhagens cancerígenas, selecionou-se o modelo obtido a partir do algoritmo de “Random Forest” como aquele com maior precisão entre os restantes, tomando esta o valor de \(63\%\).
Este valor é subótimo para a performance de um algoritmo de machine learning, contudo, pode ser melhorado com a adição de mais entradas de dados, ou com enriquecimento de genes ou de outras variáveis que permitam melhor classificar estas classes.

6.2.6 Importância das variáveis

## 
## Recursive feature selection
## 
## Outer resampling method: Cross-Validated (10 fold) 
## 
## Resampling performance over subset size:
## 
##  Variables Accuracy  Kappa AccuracySD KappaSD Selected
##          1   0.5806 0.1426    0.02692 0.04867         
##          2   0.6648 0.3005    0.07813 0.15471         
##          3   0.6973 0.3614    0.06127 0.13807         
##          4   0.7172 0.4052    0.04194 0.09405         
##          5   0.7175 0.4024    0.06071 0.13420         
##          6   0.7397 0.4453    0.04556 0.10623         
##          7   0.7469 0.4575    0.05431 0.12263         
##          8   0.7417 0.4453    0.07228 0.17200         
##          9   0.7367 0.4382    0.06721 0.15413         
##         10   0.7364 0.4312    0.06983 0.16436         
##         20   0.7619 0.4828    0.09205 0.21149         
##         40   0.7590 0.4806    0.08310 0.17725         
##         60   0.7864 0.5387    0.08202 0.17876        *
##         80   0.7688 0.4979    0.07998 0.17628         
##        100   0.7864 0.5361    0.08368 0.18491         
## 
## The top 5 variables (out of 60):
##    ENSG00000231864, ENSG00000184307, ENSG00000271580, ENSG00000224271, ENSG00000170293
##     query significant     p_value term_size query_size intersection_size
## 1 query_1        TRUE 0.003506219         2         32                 2
## 2 query_1        TRUE 0.013606114       327         32                 6
## 3 query_1        TRUE 0.013844862       328         32                 6
## 4 query_1        TRUE 0.014087002       329         32                 6
## 5 query_1        TRUE 0.020997309         4         32                 2
## 6 query_1        TRUE 0.042954982       397         31                 5
## 7 query_1        TRUE 0.035644200        10         30                 2
## 8 query_1        TRUE 0.038914221       167         30                 4
##    precision     recall    term_id source
## 1 0.06250000 1.00000000 GO:1904328  GO:BP
## 2 0.18750000 0.01834862 GO:0030198  GO:BP
## 3 0.18750000 0.01829268 GO:0043062  GO:BP
## 4 0.18750000 0.01823708 GO:0045229  GO:BP
## 5 0.06250000 0.50000000 GO:1990764  GO:BP
## 6 0.16129032 0.01259446 GO:0062023  GO:CC
## 7 0.06666667 0.20000000 GO:0098973  GO:MF
## 8 0.13333333 0.02395210 GO:0005201  GO:MF
##                                                   term_name
## 1                   regulation of myofibroblast contraction
## 2                         extracellular matrix organization
## 3                      extracellular structure organization
## 4             external encapsulating structure organization
## 5                                 myofibroblast contraction
## 6                  collagen-containing extracellular matrix
## 7 structural constituent of postsynaptic actin cytoskeleton
## 8               extracellular matrix structural constituent
##   effective_domain_size source_order      parents
## 1                 21026        23353 GO:19031....
## 2                 21026         6674 GO:00430....
## 3                 21026        10414   GO:0016043
## 4                 21026        11178   GO:0016043
## 5                 21026        24840   GO:0070252
## 6                 22149         2296   GO:0031012
## 7                 20246         8535 GO:00052....
## 8                 20246         1321   GO:0005198

Por último, foi realizada a seleção de atributos para o dataset considerado para machine learning, através do método de Recursive Feature Elimination. Este algoritmo foi implementado com uma estimação do erro correspondente a validação cruzada 10 folds.
Através do argumento “sizes”, foi dado ao algoritmo o tamanho das amostragens de variáveis a testar. Foi então determinado que dos \(100\) genes fornecidos, \(4\) permitiam uma melhor precisão do algoritmo.
A análise das designações destes genes revelam-nos, consistentemente, um conjunto de genes predominantemente ligados a funções relacionadas com a membrana celular e com tecidos epiteliais, o que é consistente com as análises anteriores.

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